Nug 26

nauty and Traces Users Guide (Version 2.
6)
Brendan D. McKay
Adolfo Piperno
Research School of Computer Science

Australian National University
Canberra ACT 0200, Australia
[email protected]
Departimento di Informatica
Sapienza Universit`a di Roma
Rome, Italy
[email protected]
August 19, 2016
Contents
0.
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
How to use this Guide.

Introduction.
The dreadnaut program.
Data structures.
Size limits.
Options and statistics.
Calling nauty and Traces.
Description of the procedure parameters.
Interpretation of the output.
User-defined procedures.
Vertex-invariants.
Writing programs which call dense nauty.
Writing programs which call sparse nauty.
Writing programs which call Traces.
Variations.
Utilities (gtools).
Installing nauty and Traces.
Recent changes.
More on automorphism groups.
Graph formats used by the utilities.
Other ways to use nauty.
Licence details.
Acknowledgements.
Help texts for the utilities.
References.
Research supported by the Australian Research Council.
How to use this Guide
nauty (no automorphisms, yes?) is a set of procedures for determining the automorphism
group of a vertex-coloured graph, and for testing graphs for isomorphism. Traces is an
alternative program for these operations.
The dreadnaut program provides sufficient functionality that most simple applications can be managed without the need to write any programs. Section 2 is intended to
be a fairly self-contained introduction to that level of use. You should start by reading
Section 1 and Section 2.
nauty and Traces also come with a set of utilities suitable for processing files of
graphs; these are described in Section 15.
For other serious purposes, you will need to write a program that calls nauty or
Traces. In that case you dont have much choice but to read this Guide from start to
finish. However, it isnt really as hard as it sounds; see the sample programs in this guide
for a constructive proof.
The current versions of nauty and Traces are available at
http://cs.anu.edu.au/bdm/nauty and http://pallini.di.uniroma1.it. There is
also a mailing list you can subscribe to if you want to discuss nauty and Traces and
receive upgrade notices: http://mailman.anu.edu.au/mailman/listinfo/nauty.
nauty and Traces are written in a highly portable subset of the language C. Modern
C compilers for most types of computer should be able to handle them without difficulty.
The theoretical basis of the original edition of nauty first appeared in [9]. An updated
account, and a detailed description of Traces appears in [10].
Introduction
nauty and Traces come with a primitive interactive interface dreadnaut which will
suffice for most one-off computations. This chapter describes the basic concepts and gives
examples of dreadnaut usage. Later chapters will describe the programming interface.
A graph for our purposes has a finite set of vertices, and a finite set of edges. Most of
the time when we write graph we mean simple undirected graph, which implies that
each edge is an unordered pair vw of distinct vertices (so multiple edges and loops are
not included).
The following shows a graph with 8 vertices and 12 edges.
An automorphism of a graph is a permutation of the vertex labels so that the set of

2
edges remains the same. In the above graph we can interchange vertex labels 0,1 and
interchange vertex labels 2,3, and this preserves the edge set (for example, 2 is adjacent
to 5 before and after, while 0 is not adjacent to 4 before or after). This means that
(0 1)(2 3) is an automorphism.
(0 1)(2 3)
1
The application of two automorphisms one after the other is an automorphism too.
The set of all automorphisms, including the trivial one (that moves no labels at all), is
called the automorphism group of the graph. The automorphism group of the graph above
has 8 automorphisms:
(1)
(0 1)(2 3)
(4 5)(6 7)
(0 1)(2 3)(4 5)(6 7)
(0 6)(1 7)(2 4)(3 5)

(0 7)(2 5)(1 6)(3 4)
(0 6 1 7)(2 4 3 5)
(0 7 1 6)(2 5 3 4)
Because the number of automorphisms can be extremely large, it is more efficient to

work with a set of generators of the automorphism group. This is a set of automorphisms
such that every automorphism can be expressed as a combination of them. In the example,
a set of generators is {(4 5)(6 7), (0 6)(1 7)(2 4)(3 5)}.
The automorphisms also define an equivalence relationship on the vertices of the graph:
two vertices are equivalent if there is an automorphism taking one to the other. For
example, vertices 6 and 7 are equivalent since the automorphism (4 5)(6 7) takes 6 onto 7.
The sets of equivalent vertices are called orbits; in the example they are {0, 1, 6, 7} and
{2, 3, 4, 5}.
Another function that nauty and Traces can perform is canonical labelling. This is
an operation of placing the vertex labels in a way that does not depend on where they were
before. Graphs that are isomorphic (the same except for vertex labels) become identical
(exactly the same) after canonical labelling (canonizing).
In the figure below, the two graphs in the upper row are clearly isomorphic, though
they are not identical (for example 0 and 4 are adjacent in the left graph but not in the
right graph). However, when the graphs are canonized, producing the graphs in the lower
3
row, the results are identical (note that the edges of the two graphs are the same, even
though the drawings differ).
different
canonize
canonize
same
The purpose of canonical labelling is to test isomorphism: two isomorphic graphs

become identical when they are canonically labelled.
Sometimes the vertices of a graph are distinguished from each other according to some
criterion coming from the application. To handle this situation, vertices in nauty and
Traces can be coloured. The definition of automorphism respects colours: each vertex
can only be mapped onto a vertex of the same colour. The example below has two vertex
colours, black () first and white () second.
6
first colour
second colour
There are now only 4 automorphisms, namely those which preserve the colouring:
(1)
(4 5)(6 7)
(0 1)(2 3)
(0 1)(2 3)(4 5)(6 7)
nauty and Traces consider the colours to come in some order; i.e., there is a 1st
colour, a 2nd colour, etc.. This doesnt matter with regard to automorphisms, but it
plays an important part in canonical labelling: the new vertex labels are in order of
colour. The vertices of the first colour are labelled first, of the second colour next, and so
on. This rule means that the canonical labelling can be used to determine if two coloured
graphs are isomorphic via an isomorphism that maps each vertex of one graph onto a
vertex of the same colour in the other graph.
A colouring of the vertices is also referred to as a partition, and the colour classes as
the cells of the partition.
different
canonize
canonize
different
nauty can also handle directed graphs and loops, but Traces currently only handles
simple undirected graphs.
dreadnaut
dreadnaut is a simple program which can read graphs and execute nauty or Traces. It
is a rather primitive interface with few facilities.
Input is taken from the standard input and output is sent to the standard output, but
this can be changed by using the < and > commands. Commands may appear any
number per line separated by white space, commas, semicolons or nothing. They consist
of single characters, except when they consist of two characters. Sometimes commands
are followed by parameters.
At any point of time, dreadnaut knows the following information:
(a) The mode, which is one of dense (for using the dense version of nauty; this is
the default), sparse (for using the sparse version of nauty) and Traces (for using
Traces).
(b) The number of vertices, n.
(c) The current graph g, if defined.
(d) The current partition . If it is not defined, it is assumed equal to the partition
with every vertex in the same cell (i.e., with the same colour).
(e) The orbits of the (coloured) graph (g, ), if defined.
(f) The canonically labelled isomorph of g, called h, if defined. (Also called canong.)
(g) An extra graph called h0 , if defined. (Also called savedg.)
(h) Values for each of a variety of options.
In the following # is an integer and = is always optional.
5
(A) Commands that set the mode.

Ad or An Change the mode to dense. The dense adjacency matrix data structure will
be used for g and the dense version of nauty will be used for the x command. The
graphs g, h, h0 and the partition become undefined.
As
Change the mode to sparse. The adjacency list data structure will be used for g
and the sparse version of nauty will be used for the x command. The graphs g, h,
h0 and the partition become undefined.
At
Change the mode to Traces. The adjacency list data structure will be used for g
and Traces will be used if the x command. The graphs g, h, h0 and the partition
become undefined.
Ad+,As+,At+ As well as changing the mode, if g is defined it is converted to the data

structure required by the new mode. The graphs h and h0 become undefined, but
the partition and the orbits of g are maintained if they are defined.
The initial mode is dense.
(B) Commands which define or examine the graph g.
n =#
Set value of n. The maximum value depends on available memory.
Read the graph g.

There is always a current vertex which is initially the first vertex. (Vertices are
numbered from 0 unless you have used the $ command.) The number of the current
vertex is displayed as part of the prompt, if any. Available subcommands:
# : add an edge from the current vertex to the specified vertex. (Unless you have
selected the option digraph, edges only need to be entered in one direction.)
-# : delete the edge, if any, from the current vertex to the specified vertex.
; : increment the current vertex. If it becomes too high for a vertex label, stop.
#: : make the specified vertex the current vertex.
? : display the neighbours of the current vertex (dense mode only).
. : stop.
! : ignore the rest of this input line.
, : ignored.
Edit the graph g. The available subcommands are the same as for the g command.
This is only available in dense mode.
r . . . ; Relabel the graph g, where . . . is a permutation of {0, 1, . . . , n1}, specifying

the order in which to relabel the vertices, followed by a semicolon. Missing numbers
are filled in at the end in numerical order. For example, for n = 5, r 4,1; is
equivalent to r 4,1,0,2,3;. The partition is permuted consistently.
r&
Relabel the graph g in order of the partition , and permute consistently.
R . . . ; This is the same as r except that unspecified vertices are not filled in. Instead,
a subgraph corresponding to the given vertices is formed and replaces g. If the
command is given as -R, the given vertices are deleted instead. The partition is
6
reduced and relabelled consistently.

j
Relabel the graph g at random. The partition is permuted consistently.
Perform the doubling operation E(g) defined in [8]. The result in g is a regular
graph with order 2n + 2 and degree n.
s =#
Generate graph (or digraph) g at random with independent edge probabilities 1/i,
where i is the integer specified.
sr = #
Generate random regular graph g of degree i, where i is the integer specified. This
is only available in sparse and traces modes, and i cannot be more than 8.
(underscore) Replace the graph g by its complement. If there are any loops, the set
of loops is complemented too; otherwise, no loops are introduced.
(two underscores) If g is a digraph, take its converse (which reverses the direction
of all the edges). Otherwise do the same as .
Type the graph g, in an obvious format. The value of option linelength (see
l command) is taken into account. The format used is consistent with the input
format allowed by the g command. To examine just some of the graph, you can
use the ? subcommand within the e command.
This is exactly like t except that a line of the form n=n $=l g is written first,
where n is the number of vertices and l is the number of the first vertex, and a line
of the form $$ is written afterwards. This enables you to save a graph to a file and
easily restore it later: >newgraph.dre T -> will save g to the file newgraph.dre,
while <newgraph.dre will restore it.
v,vv
Display the degrees of each vertex of the graph g, if defined. For vv, a count of
how many vertices have each degree is given instead. For digraphs, the outdegrees
are displayed. Loops count as 1.
(C) Commands which define the partition .

f
Specify a partition.
-f selects the partition with only one cell, which is the default.
f = # selects the partition with one cell containing just the vertex named and one
cell containing every other vertex.
f = [ . . . ] selects an arbitrary partition. Replace . . . by a list of cells separated
by |. You can use the abbreviation x:y for the range x, x+1, . . . , y. Any
vertices not named are put in a cell of their own at the end.
Example: If n = 10, then f=[3:7 | 0,2] establishes the partition
[3, 4, 5, 6, 7 | 0, 2 | 1, 8, 9].
F =#
Make the partition finer by placing the specified vertex in a cell of its own just
before the remains of the cell it was in before.
FF
Identify the cell which would be first individualized by the chosen algorithm (according to the mode), and place one vertex of that cell in a cell of its own just before
the remains of the cell it was in before. This is not likely to be meaningful unless
the partition has been refined first (see the i command). The rule for choosing a
7
cell is the one that nauty or Traces uses at the top of the search tree; this means
that repeated use of FF doesnt necessarily follow a path that nauty or Traces
would follow.
i
Perform a refinement operation, replacing the partition by its refinement. The

refinement procedure used depends on the mode.
Perform a refinement operation, an application of the vertex-invariant (if one has

been selected using the * command), and (if any cells were split) another refinement
operation. The final partition becomes . The behaviour may be modified by the
K command, but not by the k command. This is useful for determining whether
an invariant is effective for a particular graph. Note that you need to restore the
partition between repeated tests, for example by using the f command.
If the orbits of the automorphism group are known (as by executing the x command),
they are converted into a partition . The cells of are the orbits, and they are
arranged in order of their least elements.
OO
This is like O, except that the orbits are placed in increasing order of size and equalsized orbits are combined into single cells. This means the resulting partition is an
isomorphism invariant.
(D) Commands which establish or examine options.

$ =#
Establish an origin for vertex numbering. The default is 0. Only non-negative

values are permitted. All the input-output routines used by nauty or dreadnaut
respect this value, even though internally vertices are always numbered from 0.
$$
Restore the vertex numbering origin to what it was just before the last $ command.
Only one previous value is remembered.
l =#
Set value of option linelength : the length of the longest line permitted for output.
The default value is installation-dependent (typically 78). A value of 0 indicates no
limit.
w =#
Set value of worksize : the amount of space provided for nauty to store automorphism data. The amount provided is enough to store i automorphisms, where i is
the integer provided. Traces does not use this option.
Ignored. Provided for contrast with -.
d,-d
Set option digraph to TRUE or FALSE, respectively. You must set it to TRUE if
you wish to define g to be a digraph or a graph with loops. The default is FALSE.
Changing it from TRUE to FALSE also causes the graph g to become undefined,
as a safety measure. This version of Traces cant handle either directed edges or
loops.
c,-c
Set option getcanon to TRUE or FALSE, respectively. This tells nauty or Traces
whether to find a canonical labelling or just the automorphism group. The default
is FALSE.
a,-a
Set option writeautoms to TRUE or FALSE, respectively. This tells nauty or

Traces whether to display the automorphisms it finds. The default is TRUE.
8
m,-m
Set option writemarkers to TRUE or FALSE, respectively. This tells nauty

whether to display the level markers level . . . . See Section 8 for their meaning.
The default is TRUE. Traces does not use this option.
p,-p
Set option cartesian to TRUE or FALSE, respectively. This tells nauty or

Traces to use the cartesian form when writing automorphisms. Precisely, the
automorphism is displayed as a list v1 v2 . . . vn , where v1 , v2 , . . . , vn are the
vertices of g. The default is FALSE.
y =#
Set the value of option tc level. A value of # tells nauty to use an advanced, but
expensive, algorithm for choosing target cells in the top k levels of the search tree.
See Section 7 for a more detailed description. The default is 100, but setting it to 0
might speed up the average time for easy graphs. Traces does not use this option.
G =#
Set a parameter that effects a probabilistic method (random Schreier algorithm).

G=0 turns off the method altogether (acceptable for nauty but disastrous for Traces).
Larger values make the method more precise but more expensive. The default value
is 10, which is adequate for most purposes.
S =#
Specify a strategy for Traces. Only 0 is supported in this version.
=#
Select a vertex-invariant. One user-defined vertex-invariant can be linked with

dreadnaut if its name is provided in the preprocessor variable INVARPROC. The
argument to the command is interpreted thus:
-1 : the user-defined procedure (if any)
0 : no vertex-invariant (this is the default)
1 : twopaths
2 : adjtriang
3 : triples
4 : quadruples
5 : celltrips
6 : cellquads
7 : cellquins
8 : distances (all modes)
9 : indsets
10 : cliques
11 : cellcliq
12 : cellind
13 : adjacencies (all modes)
14 : cellfano
15 : cellfano2
16 : refinvar
These procedures are described in Section 10. The default behaviour is for the
invariant to be applied only at the root of the tree, but this can be modified using
the k command. The K command can be used to change the invariant parameter, if
there is one. The default is K=3 for indsets, cliques, cellind and cellcliq; and
K=0 for everything else. Except where indicated, the invariants are only available in
dense mode. See the k command for restrictions in Traces mode.
k = # # (Two integer arguments.) Define values for the options mininvarlevel and
maxinvarlevel. These tell nauty the minimum and maximum levels of the tree
at which it is to apply the vertex-invariant. The root of the tree is at level 1. See
Section 7 for a little more information about these options. The default is k = 0 1,
which causes the invariant to be applied only at the top of the search tree. Traces
does not use invariants itself, but invariants will be applied before calling Traces if
mininvarlevel 1 maxinvarlevel.
K =#
Give a value to the invararg option. This number is passed to the vertex-invariant
by the I command and by nauty. See Section 10 for the meaning of this option for
each available vertex-invariant. The default value depends on the invariant; see the
command.
V =#
Specify a verbosity level for Traces. A value of 0 means that no output will be
written except for group generators (according to the c command) and the summary
at the end. Values greater than 0 produce more and more output during execution,
see Section 8. The default is 0.
u =#
Request calls to user-defined functions (nauty only). The value is

1 for usernodeproc,
2 for userautomproc,
4 for userlevelproc,
16 for userrefproc,
32 for usercanonproc.
These can be added together to select more than one procedure. The procedures
called are those named by the compile-time symbols USERNODE, USERAUTOM,
USERLEVEL, USERREF and USERCANON defined in dreadnaut.c. The default
values are:
USERNODE: For each node, print a number of dots equal to the depth, then
(numcells/code/tc) where numcells is the number of cells, code is the code produced by the refinement procedure, and tc is the position in lab where the target
cell starts. For the first path down the tree, the partition is displayed as well.
USERAUTOM: For each automorphism, display the arguments numorbits and
stabvertex (see Section 9).
USERLEVEL: For each level, display the arguments tv, index, tcellsize, numcells
and childcount, as well as the fields numnodes, numorbits and numgenerators of
stats. See Section 9 for what they mean.
USERREF: Do nothing.
USERCANON: Each time the canonical labelling is updated, print the sequence
number and the refinement code.
Type the mode, and the current values of m, n, worksize, most of the options, the
number of edges in g, and the number of cells in . If output has been directed
away from stdout using the > command, some of this information is also written
to stdout.
&
Type the current partition , unless it is has only one cell.
&&
Same as &, except that the quotient of g with respect to is also written. Say
10
= (V0 , V1 , . . . , Vm ) and let vi be the least numbered vertex in Vi for 0 i m.

Then, for each i, this command writes vi , then |Vi | in brackets, then the numbers
k0 , k1 , . . . , km , where kj is the number of edges from vj to Vi . The value 0 is written
as -, while the value |Vi | is written as .
P,-P
Turn on, respectively off, the facility to provide known automophisms to Traces.
If this is turned on, the PP command (below) can be used to input automorphisms,
and the group generators (including the extra ones found by Traces) are kept when
Traces exits. The generators will be deleted if the graph changes. To delete them
manually, use -P P (with the space!).
PP...; Set on the facility to provide known automophisms to Traces (if it isnt on
already) and read in one automorphism. Use of this command one or more times
before command x in Traces mode allows known automorphisms to be given to
Traces. When Traces runs, it checks whether the permutation is in fact an automorphism, and dies if it is not. The format of the input is a list of n distinct integers
comprising a permutation. Note that the automorphisms you give to Traces are
not written by it; only extra generators are written.
Example: If n = 7 then PP 4 0 2 3 6 5 1; is valid input.
(E) Commands which execute nauty or Traces or use the results.
x
Execute nauty or Traces. The program to execute depends on the mode.

Depending on the values of the writeautoms and writemarkers options, the automorphism group will be displayed while nauty or Traces is running. See Section 8
for an explanation of the output. If getcanon is TRUE, a canonically labelled graph
is computed too. When nauty or Traces returns, dreadnaut will display some
statistics about its execution. See Section 7 for the meanings; the important ones
are the order of the group and the number of orbits. Depending on your system,
the execution time is also displayed.
Copy h, if defined, to h0 . See the description of the # command for more.
Type the canonical label and the canonically labelled graph. The canonical label is
given in the form of a list of the vertices of g in canonical order. Only possible after
x with option getcanon selected.
Type three 8-digit hex numbers whose value depends only on h. This allows
quick comparison between graphs. Isomorphic graphs give the same value. Nonisomorphic graphs may also give the same value, though this is rare. Only possible
after x with option getcanon selected.
Compare the labelled graphs h and h0 . Both must have been already defined (using
x and @). The complete process for testing two graphs g1 and g2 for isomorphism is
this:
enter g1
c x @
(select getcanon option, execute nauty or Traces, copy h to h0 );
enter g2
x #
(execute nauty or Traces, compare h to h0 ).
11
##
This is the same as # except that, if h is identical to h0 , you will also be given an
isomorphism from g1 to g2 . This is in the form of a sequence of pairs vi -wi , where
vi is a vertex of g1 and wi is a vertex of g2 . The vertex-numbering origin in force
when h0 was created is used for g1 , whilst the origin now in force is used for g2 .
Type the orbits of the group. Only possible after x. For orbits longer than one
vertex, the orbit size is shown in parentheses.
M = #,M = #/#,-M Each call to nauty or Traces is repeated until either the number of
repetitions exceeds the first value or (if the second part is included) the cpu time
exceeds the number of seconds in the second value. Each limit can be turned off by
setting the value to 0. The cpu time is then reported accurately. This is for doing
timing tests with easy graphs. Output is suppressed except for the first execution.
This also effects the i command. -M and M=1 turn this feature off.
(F) Miscellaneous commands.
h,H
Help: type a summary of dreadnaut commands.
"..." Anything between the quotes is simply copied to the output. The ligatures \n
(newline), \t (tab), \b (backspace), \r (carriage return), \f (formfeed), \\
(backslash), \ (single quote) and \" (double quote) are recognised. Other occurrences of \ are ignored.
!
Ignore anything else on this input line. Note that this is a command, not a comment
character in the usual sense, so you cant use it in the middle of other commands.
<
Begin reading input from another file. The name of the file starts at the first nonwhite character after the < and ends before the next white character, unless the
first non-white character is " in which case the name ends at the next " or
newline. If such a file cannot be found, another attempt is made with the string
.dre appended to the name. When end-of-file is encountered on that file, continue
from the current input file. The allowed level of nesting is configurable (usually 10).
>,>>
Close the existing output file unless it is the standard output, then begin writing
output to another file. The name of the file starts at the first non-white character
after the > and ends before the next white character, unless the first non-white
character is " in which case the name ends at the next " or newline. For >
the file starts off empty. For >>, if an existing file of the right name exists, it is
written to starting at the current end-of-file.
->
If an output file other than standard output is in use, close it and direct output
back to the standard output.
->>
Flush the output file.
B,-B
Turn flushing on or off. Initially it is off. When flushing is on, the output will be
flushed at the end of every command.
Quit. dreadnaut will exit irrespective of which level of input nesting it is on.
12
(G) Command line options

Some dreadnaut commands can be given on the command line using the -o switch;
for example dreadnaut -o "At c -a G=20". Only one such string of commands is
allowed. The available commands are:
Ad, As, At, a, c, d, G, l, m, M, p, P, V, w, y, $,
and negatives of those such as -c.
(H) Signal processing
If a SIGINT signal is received while nauty or Traces is executing, they will be
aborted without aborting dreadnaut. On UNIX-like systems, this can be achieved by
typing control-C. If such a signal is received at any other time, dreadnaut is aborted.
The canonical labellings produced by dreadnaut can depend on the values of many
of the options. If you are testing two or more graphs for isomorphism, it is important that
you use the same values of these options for all your graphs. In general, h is a function
of all these:
(a) the mode
(b) option digraph (d command)
(c) all the vertex-invariant options (, k and K commands)
(d) the value of tc level (y command)
(e) the version of nauty or Traces used
Assuming you dont have a particularly ancient or broken compiler, the canonical
labelling does not depend on the compiler, the operating system, the hardware, or the
word size.
2.1
Sample dreadnaut sessions
Several sample dreadnaut sessions are shown below. The underlined characters are those
typed by the user.
3
2
g =
4
5
6
7
> n=8 g
0: 1 3 4;
1: 2 5;
2: 3 6;
3: 7;
8 vertices
enter the graph
13
4: 5 7;
5: 6;
6: 7.
> f=2 x
fix vertex 2; execute
[fixing partition]
(0 5)(3 6)
level 2: 6 orbits; 3 fixed; index 2
(1 3)(5 7)
4 orbits; grpsize=6; 2 gens; 6 nodes; maxlev=3
cpu time = 0.00 seconds
> o
show the orbits
0 5 7 (3); 1 3 6 (3); 2; 4;
> q
quit
The next problem solved is to determine an isomorphism between the following two
graphs. We turn off the writing of automorphisms to save some space, and this time we
will use Traces.
11
8
g1 =
2
11
10
3
2
4
g2 =
10
> At
use Traces mode
> c -a V=0
turn getcanon on, group writing and verbosity off
> n=12 g
enter the first graph
0: 1; 2; 0;
3: 4; 5; 6; 3;
7: 8; 9; 10; 11; 7.
> x @
execute, save the result
3 orbits; grpsize=480; 4 gens; 41 nodes (1 interrupted); maxlev=6;
canupdates=1; cpu time = 0.00 seconds
> g
enter the second graph
0: 1; 2; 3; 4; 0;
5: 6; 7; 8; 5;
9: 10; 11; 9.
> x
execute
3 orbits; grpsize=480; 5 gens; 35 nodes (2 interrupted); maxlev=6;
compare to saved graph
> ##
14
h and h are identical.

0-9 1-10 2-11 3-5 4-6 5-7 6-8 7-0 8-1 9-2 10-3 11-4
> q
quit
As a third example, we consider a simple block design. nauty and Traces can compute automorphisms and canonical labellings of block designs by the common method of
converting the design to an equivalent coloured graph. Suppose a design D has varieties
x1 , x2 , . . ., xv and blocks B1 , B2 , . . ., Bb . Define G(D) to be the graph with vertex set
{x1 , . . . , xv , B1 , . . . , Bb }, with each x-vertex having one colour and each B-vertex having
a second colour, and edge set {xi Bj | xi Bj }. The following theorem is elementary.
Theorem 1.
(a) The automorphism group of D is isomorphic to the automorphism group of G(D).
(b) If D1 and D2 are designs, D1 and D2 are isomorphic if and only if G(D1 ) and
G(D2 ) are isomorphic.
Consider the design D = { {1, 2, 4}, {1, 3}, {2, 3, 4} }. Label G(D) so that the varieties
of D correspond to vertices 14, while the blocks correspond to vertices 57. This time
we will do it with the sparse version of nauty.
1
2
g =
3
4
5
6
7
> $=1 As
label vertices starting at 1, sparse mode
> n=7 g
1: 5:
go to vertex 5 (block 1), the character is a colon
5: 1 2 4;
6: 1 3;
7: 2 3 4.
> f=[1:4]
fix the varieties setwise
> cx
run nauty
[fixing partition]
(2 4)
group generators
(1 3)(5 7)
4 orbits; grpsize=4; 2 gens; 6 nodes; maxlev=3
> o
display the orbits
1 3 (2); 2 4 (2); 5 7 (2); 6;
> b
display the canonical labelling
2 4 1 3 6 7 5
the vertices in canonical order
15
1
2
3
4
5
6
7
> q
:
:
:
:
:
:
:
6
6
5
5
3
1
1
the relabelled graph
7;
7;
7;
6;
4;
2 4;
2 3;
quit
Looking at the vertices 5,6,7 which represent the blocks, we see that the canonically
labelled block design is { {3, 4}, {1, 2, 4}, {1, 2, 3} }.
Data Structures
In this section we will describe the basic data structures required for programs that call
nauty or Traces.
Data structure for graphs.
There are two graph data structures supported. One is the dense form (also called the
packed form) used only by the dense version of nauty. The other is the sparse form used
by the sparse version of nauty and by Traces. The vertices of a graph are numbered
0, 1, . . . , n 1.
The dense form of a graph is an adjacency matrix with one bit per entry. A setword
is an unsigned integer type of either 16, 32 or 64 bits, depending on the compile-time
parameter WORDSIZE. (By default, WORDSIZE is 32 unless the size of type long int
is greater than 32, in which case WORDSIZE is 64, but this test can be overridden at
configuration time, see Section 16.)
A set (by which we always mean a subset of V = {0, 1, . . . , n1}) is represented by
an array of m setwords, where m is some number such that WORDSIZE m n. The
bits of a set are numbered 0, 1, . . . , n1 left to right (within each setword: high order
to low order). Bits which dont get numbers are called unnumbered and are assumed
permanently zero. A set represents the subset { i | bit i is 1 }.
A graph represented in dense form uses the type graph. It is stored as an array of n
sets (so it has mn setwords altogether). The i-th set gives the vertices to which vertex
i is adjacent, for 0 i < n.
The C types setword, set and graph are actually the same, so a graph in dense form
is really represented by a 1-dimensional array of length mn, not by an array of arrays.
A graph represented in sparse form uses the type sparsegraph. It is stored as a
structure with the following fields:
int nv: the number of vertices
size t nde: the number of directed edges (loops count as 1, other undirected edges as 2)
size t v: pointer to an array of length at least nv
16
int d: pointer to an array of length at least nv

int e: pointer to an array of length at least nde
sg weight w: not used in this version, should be NULL
size t vlen, dlen, elen, wlen: the actual lengths of the arrays v, d, e and w. The unit
is the element type of the array in each case (so vlen is the number of entries of
type size t in the array v, etc.) In this version, wlen should be 0.
For each vertex i = 0 . . . n1, d[i] is the degree (out-degree for a digraph) of that vertex. v[i] is an index into the array e such that e[v[i]],e[v[i]+1],. . .,e[v[i]+d[i]-1]
are the vertices to which vertex i is joined. It is not necessary that this list of neighbours
be sorted. These neighbour lists can be present in the array e in any order and may have
gaps between them, but cannot overlap. If d[i]=0 for some i, v[i] is not used.
2
0
0110 0
1000 0
1000 0
2
0
1
0010 0
1100 0
1000 0
nv
nde
d
v
e
dlen
vlen
elen
3
4
nv
nde
d
v
e
dlen
vlen
elen
3
4
2 1 1
0 3 5
5
3
7
&
1 2
1 2 1
0 2 4
4
3
5
&
0 1 0
Figure 1: Dense and sparse data structures for graphs and digraphs.
In Figure 1, the graph on the left is represented in dense form by the array in the
centre (we show three words of type setword). On the right is a possible sparse form for
the same graph. Note that loops are only allowed for directed graphs, and contribute 1
to the vertex degree.
Before the sparesgraph structure can be used, it needs to be initialised. Fields
d,v,e,w should be set to NULL, and dlen,vlen,elen,wlen should be set to 0. After
initialisation, the sizes of the fields will be automatically adjusted as required, so you
dont need to initialise it again.
Data structure for permutations, orbits, and colourings.
A permutation of V is represented by an array of n integers, type int, with the i-th
entry giving the image of i under the permutation.
17
The orbits of the automorphism group is also represented by an array of n integers,

type int. The value of the i-th entry is the smallest number of a vertex in the same orbit
as vertex i.
Examples of a permutation and a set of orbits for n = 9 are given below.
2 3 5 6 1 0
4 7 8
is the permutation (0 2 5)(1 3 6 4)
0 0 2 2 0 0
6 2 6
gives the orbits {0, 1, 4, 5}, {2, 3, 7}, {6, 8}
A colouring (partition) of the vertices is specified by a pair of arrays, usually called

lab and ptn. The array lab contains a list of the vertices in some order. The array
ptn indicates the division into colours: if ptn[i] = 0, then a cell (colour class) ends at
position i. The following example for n = 9 shows one way to represent the partition
[{2}, {3}, {0, 1, 5, 6}, {4, 7, 8}].
lab: 2
3 5 6 1 0 4
7 8
all vertices in some order
ptn: 0
0 1 1 1 0 1
1 0
cells end where the zeros are
Note that colours come in a particular order. In the example, there are 4 colours listed
left to right. However, each colour class by itself is an unordered set of vertices so it makes
no difference which order they are listed in. Also, values in ptn which are not 0 can be
any positive value. (Advanced hint: this is not true internally to nauty, probably you
dont need to know this.) So, for example, exactly the same partition is represented by
the following.
lab: 2
3 1 6 5 0 7
8 4
all vertices in some order
ptn: 0
0 1 2 2 0 8
3 0
cells end where the zeros are
The type boolean is a synonym for int, but the different name is intended to encourage
you to restrict the values to either TRUE or FALSE (which are defined as 1 and 0,
respectively).
Size limits
There are several ways to compile nauty, leading to differences in types and the size of
graph that can be processed. These are selected by preprocessor variables.
(1) If type int has less than 32 bits (very rare these days), there is an absolute limit of
215 3 = 32765.
(2) If type int has at least 32 bits, there is an absolute limit of 2 109 on the order of
a graph.
In addition, there is a choice between static and dynamic memory allocation for the
larger data objects. This is selected by the value of the preprocessor variable MAXN.
18
(a) If MAXN is defined as 0, the limit on the order of a graph is given in (1)(2) above
and objects are dynamically allocated. Of course, if you dont have enough memory,
dynamic allocation may fail. This is the default.
(b) If MAXN is defined as a positive integer, that is the limit on the order of a graph.
It cant be greater than the absolute limit given in (1)(2) above. In this case most,
but not all objects are statically allocated, so space is wasted if MAXN is much
larger than what is actually used.
A special case of option (b) is 0 < MAXN WORDSIZE, which implies that a set
consists of a single setword. Some of the critical routines in nauty have special code to
optimize performance in that case. The recommended way to compile for this case is to
define MAXN to be the name WORDSIZE.
Traces is limited to the same number of vertices as nauty, including the restriction
to MAXN if that is non-zero.
Options and statistics
Various options are provided to nauty or Traces by means of options structures. The
type optionblk is used for nauty and the type TracesOptions for Traces.
In all cases, it is strongly recommended that the values be first set to their defaults
by using one of the provided macros:
DEFAULTOPTIONS GRAPH : for undirected graphs in dense nauty
DEFAULTOPTIONS DIGRAPH : for digraphs in dense nauty
DEFAULTOPTIONS SPARSEGRAPH : for undirected graphs in sparse nauty
DEFAULTOPTIONS SPARSEDIGRAPH : for digraphs in sparse nauty
DEFAULTOPTIONS TRACES : for undirected graphs in Traces
If any of the defaults are not suitable, change them using assignment statements. In this
way you will only need to recompile if the option structures change in the future.
We first describe optionblk, used by nauty (both dense and sparse versions).
boolean getcanon: If this is TRUE, the canonically labelled graph is produced as well as
the automorphism group. Otherwise, only the automorphism group is determined.
Default FALSE.
boolean digraph: This must be TRUE if the graph has any directed edges or loops. If no
directed edges or loops are present, selecting this option is legal but may degrade the
performance slightly and the canonical labelling might be different. Default TRUE
for DEFAULTOPTIONS DIGRAPH and DEFAULTOPTIONS SPARSEDIGRAPH,
otherwise FALSE.
boolean writeautoms: If this is TRUE, generators of the automorphism group will be
written to the file outfile (see below). The format will depend on the settings
of options cartesian and linelength (see below, again). More details on what
19
is written can be found in Section 8. Default FALSE (but dreadnaut sets it to

TRUE).
boolean writemarkers: If this is TRUE, extra data about the automorphism group
generators will be written to the file outfile (see below). An explanation of what
these data are can be found in Section 8. Default FALSE (but dreadnaut sets it to
TRUE).
boolean defaultptn: If this is TRUE, it is assumed that all vertices of the graph have
the same colour (so the initial values of the parameters lab and ptn are ignored).
If it is FALSE, the initial colouring of the vertices is determined by lab and ptn as
described above. Default TRUE.
boolean cartesian: If writeautoms = TRUE, the value of this option effects the format
in which automorphisms are written. If cartesian = FALSE, the output is the
usual cyclic representation of , for example (2 5 6)(3 4). If cartesian = TRUE,
the output for an automorphism is the sequence of numbers 1 2 . . . (n1) ,
for example 1 5 4 3 6 2. Default FALSE.
int linelength: The value of this variable specifies the maximum number of characters per line (excluding end-of-line characters) which may be written to the file
outfile (see below). Actually, it is ignored for the output selected by the option
writemarkers, but that never has more than about 65 characters per line anyway.
A value of 0 indicates no limit. Default 78.
FILE outfile: This is the file to which the output selected by the options writeautoms
and writemarkers is sent. It must be already open and writable. The null pointer
NULL is equivalent to stdout (the standard output). Default NULL.
void (userrefproc)(): This is a pointer to a user-defined procedure which is to be
called in place of the default refinement procedure. Section 9 has details. If the
value is NULL, the default refinement procedure is used. Default NULL.
void (userautomproc)(): This is a pointer to a user-defined procedure which is to be
called for each generator. Section 9 has details. No calls will be made if the value
is NULL. Default NULL.
void (userlevelproc)(): This is a pointer to a user-defined procedure which is to be
called for each node in the leftmost path downwards from the root, in bottom to
top order. Section 9 has details. No calls will be made if the value is NULL. Default
NULL.
void (usernodeproc)(): This is a pointer to a user-defined procedure which is to be
called for each node of the tree. Section 9 has details. No calls will be made if the
value is NULL. Default NULL.
int (usercanonproc)(): This is a pointer to a user-defined procedure which is to be
called for each leaf of the tree which is the best labelling so far. The value returned
will effect nauty behaviour. Section 9 has details. No calls will be made if the value
is NULL or getcanon is FALSE. Default NULL.
void (invarproc)(): This is a pointer to a vertex-invariant procedure. See Section 10
for a discussion of vertex-invariants. No calls will be made if the value is NULL.
20
The default is adjacencies for DEFAULTOPTIONS DIGRAPH, adjacencies sg

for DEFAULTOPTIONS SPARSEDIGRAPH, and NULL otherwise.
int tc level: Two rules are available to choose target cells. On levels up to level
tc level, inclusive, an expensive but (empirically) highly effective rule is used.
(The root of the search tree is at level one.) At deeper levels, a cheaper rule is used.
For difficult graphs, a large value is recommended. For easier graphs, use 0. Default
100.
int mininvarlevel: The absolute value gives the minimum level at which invarproc
will be applied. (The root of the search tree is at level one.) If option getcanon =
FALSE, a negative value indicates that the minimum level will be automatically set
by nauty to the least level in the left-most path in the search tree where invarproc
is applied and refines the partition. If getcanon = TRUE, the sign is ignored. A
value of 0 indicates no minimum level. Default 0.
int maxinvarlevel: The absolute value gives the maximum level at which invarproc
will be applied. (The root of the search tree is at level one.) If option getcanon =
FALSE, a negative value indicates that the maximum level will be automatically set
by nauty to the least level in the left-most path in the search tree where invarproc
is applied and refines the partition. If option getcanon = TRUE, the sign is ignored.
A value of 0 effectively disables invarproc. Default 1.
int invararg: This value is passed by nauty to the vertex-invariant procedure invarproc,
which might use it for any purpose it pleases. Default 0.
dispatchvec dispatch: This is a vector of procedure pointers used to implement different versions of nauty. The defaults depend on which DEFAULTOPTIONS variant
is used.
boolean schreier: If this is TRUE, pruning of the search tree will be enhanced by
use of the random Schreier algorithm. Default FALSE (but dreadnaut sets it to
TRUE). The setting of this parameter does not effect the canonical labelling.
We now describe TracesOptions, used by Traces.
boolean getcanon: If this is TRUE, the canonically labelled graph is produced as well as
the automorphism group. Otherwise, only the automorphism group is determined.
Default FALSE.
boolean writeautoms: If this is TRUE, generators of the automorphism group will be
written to the file outfile (see below). The format will depend on the settings
of options cartesian and linelength (see below, again). More details on what
is written can be found in Section 8. Default FALSE (but dreadnaut sets it to
TRUE).
boolean cartesian: If writeautoms = TRUE, the value of this option effects the format
in which automorphisms are written. If cartesian = FALSE, the output is the
usual cyclic representation of , for example (2 5 6)(3 4). If cartesian = TRUE,
the output for an automorphism is the sequence of numbers 1 2 . . . (n1) ,
for example 1 5 4 3 6 2. Default FALSE.
21
boolean digraph: Unused, must be FALSE. This release of Traces cannot handle digraphs.
boolean defaultptn: If this is TRUE, it is assumed that all vertices of the graph have
the same colour (so the initial values of the parameters lab and ptn are ignored).
If it is FALSE, the initial colouring of the vertices is determined by lab and ptn as
described above. Default TRUE.
int linelength: The value of this variable specifies the maximum number of characters
per line (excluding end-of-line characters) which may be written to the file outfile
(see below). Default 0.
FILE outfile: This is the file to which the output selected by the options writeautoms
and verbosity is sent. It must be already open and writable. The null pointer
NULL is equivalent to stdout (the standard output). Default NULL.
int strategy: Must be 0 in this version.
int verbosity: A level of verbosity of messages while Traces is running. A value of
0 means that no output will be written (except that automorphisms are written if
the writeautoms option requests them). Larger values produce greater information about the execution, though its interpretation requires some knowledge of the
algorithm. Default 0.
permnode generators: This can be used to provide known automorphisms to Traces
and receive the automorphisms from Traces when it is finished. If it is NULL when
Traces is called, Traces does not change it. If it is non-NULL, it is expected to
point to a (perhaps empty) circular list of known automorphisms. (It is an error to
give a permutation that is not an automorphism of the input coloured graph.) In this
case, Traces will add automorphisms to the list so that the whole automorphism
group is generated. See Section 18 for detailed instructions and examples. Default
NULL.
void (userautomproc) (int,int,int): This is a pointer to a user-defined procedure
which is to be called for each generator. Section 9 has details. No calls will be made
if the value is NULL. Default NULL.
Structured types for receiving statistics
nauty and Traces provide some statistics on output. These values do not play a part
in the computation, so it isnt an error if some of the counts exceed the capacity of the
fields they are stored in.
The various fields of a structure of type statsblk are set by nauty. Their meanings
are as follows:
double grpsize1, int grpsize2: Within rounding error, the order of the automorphism group is equal to grpsize1 10grpsize2 . If the exact size of a very large
group is needed, it can be calculated from the output selected by the writemarkers
option, or you can compute it with your own multiprecision arithmetic using the
userlevelproc feature. See Section 8.
int numorbits: The number of orbits of the automorphism group.
22
int numgenerators: The number of generators found.

int errstatus: If this is nonzero, an exceptional condition was detected by nauty.
Possible values are:
MTOOBIG: m is too big. The maximum is 2000000000/WORDSIZE+1 if MAXN=0
and int has at least 32 bits, 32765/WORDSIZE+1 if MAXN=0 and int has at least
32 bits, and dMAXN/WORDSIZEe otherwise.
NTOOBIG: n is too big. Either n > WORDSIZE m or n exceeds its absolute
limit as in Section 4.
CANONGNIL: canong = NULL, but options.getcanon = TRUE.
nauty also writes a message to stderr in these cases.
NAUABORTED: This means that nauty was aborted under program control. The
only way of doing this at the moment is to return a non-zero value from the
usercanonproc procedure.
NAUKILLED: This means that nauty gave up because the global int variable
nauty kill request became non-zero. This happens on UNIX-like systems when
nauty is run under dreadnaut and control-C is pressed.
unsigned long numnodes: The total number of tree nodes generated.
unsigned long numbadleaves: The number of leaves of the tree which were generated
but were useless in the sense that no automorphism was thereby discovered and the
current-best-guess at the canonical labelling was not updated.
int maxlevel: The maximum level of any generated tree node. The root of the tree is
on level one.
unsigned long tctotal: The total size of all the target cells in the search tree. The
difference between this value and numnodes provides an estimate of the efficiency of
nautys search-tree pruning.
unsigned long canupdates: The number of times the programs idea of the best candidate for canonical label was updated, including the original one.
unsigned long invapplics: The number of nodes at which the vertex-invariant was
applied.
unsigned long invsuccesses: The number of nodes at which the vertex-invariant succeeded in refining the partition more than the refinement procedure did.
int invarsuclevel: The least level of the nodes in the tree at which the vertex-invariant
succeeded in refining the partition more than the refinement procedure did. The
value is zero if the vertex-invariant was never successful.
Traces returns some statistics in an argument of type TracesStats.
double grpsize1, int grpsize2: Within rounding error, the order of the automorphism group is grpsize1 10grpsize2 .
int numorbits: The number of orbits of the automorphism group.
int treedepth: The depth of the search tree.
int numgenerators: The number of generators found for the automorphism group.
23
unsigned long numnodes: The total number of tree nodes generated.

unsigned long interrupted: The number of refinement operations aborted early.
unsigned long canupdates: The number of times the programs idea of the best candidate for canonical label was updated, including the original one.
unsigned long peaknodes: The maximum number of tree nodes simultaneously existing at any moment during the execution.
int errstatus: If this is nonzero, an exceptional condition was detected by Traces.
Possible values are:
NAUKILLED: This means that Traces gave up because the global int variable
nauty kill request became non-zero. This happens on UNIX-like systems when
Traces is run under dreadnaut and control-C is pressed.
Calling nauty and Traces
In this section, we describe simplified interfaces to nauty and the main interface to
Traces. The hairy details of calling nauty directly will be left to Section 7.
A call to the dense version of nauty can be made as follows.
densenauty(g, lab, ptn, orbits, options, stats, m, n, canong)
graph g: The input graph. Read-only.
int lab,ptn: Two arrays of n entries. Their use depends on the values of several
options. If options.defaultptn = TRUE, the input values are ignored; otherwise, they define the initial colouring of the graph (see above for the format). If
options.getcanon = TRUE, the value of lab on return is the canonical labelling
of the graph. Precisely, it lists the vertices of g in the order in which they need to
be relabelled to give canong. Irrespective of options.getcanon, neither lab nor
ptn is changed by enough to change the colouring. (Recall that the order of the
vertices within the cells is irrelevant.) Read-Write.
int orbits: An array of n entries to hold the orbits of the automorphism group. When
densenauty returns, orbits[i] is the number of the least-numbered vertex in the
same orbit as i, for 0 i n1. Write-only.
optionblk options: A structure giving a list of options to the procedure. See above
for their meanings. It should be declared using DEFAULTOPTIONS GRAPH or
DEFAULTOPTIONS DIGRAPH, but options other than dispatch can be changed.
Read-only.
statsblk stats: A structure used by nauty to provide some statistics about what it
did. See above for their meanings. Write-only.
int m, n: The number of setwords in sets and the number of vertices, respectively.
It must be the case that 1 n m WORDSIZE. If nauty is compiled with
MAXN > 0, it must also be the case that n MAXN and m MAXM, where
MAXM = dMAXN/WORDSIZEe. Read-only.
24
graph canong: The canonically labelled isomorph of g produced by nauty. This argument is ignored if options.getcanon = FALSE, in which case the nil pointer
NULL can be given as the actual parameter. Write-only.
A call to the sparse version of nauty can be made as follows.
sparsenauty(g, lab, ptn, orbits, options, stats, canong)
The parameters are the same as for densenauty except:
(a) Parameters g and canong have type sparsegraph*. If options.getcanon = TRUE,
then canong should have been initialised (see Section 12). The fields will be automatically expanded if they arent large enough.
(b) options should be declared using either DEFAULTOPTIONS SPARSEGRAPH or
DEFAULTOPTIONS SPARSEDIGRAPH, but options other than dispatch can be
changed.
A call to Traces looks like this:
Traces(g, lab, ptn, orbits, toptions, tstats, canong)
sparsegraph g: The input graph. Read-only.
options. If toptions.defaultptn = TRUE, the input values are ignored (every
vertex has the same colour); otherwise, they define the initial colouring of the graph
(see above for the format). If toptions.getcanon = TRUE, the value of lab on
return is the canonical labelling of the graph. Precisely, it lists the vertices of g in
the order in which they need to be relabelled to give canong. Read-write.
int orbits: Returns the orbits of the automorphism group, as described above. Writeonly.
TracesOptions toptions: A structure giving a list of options to the procedure. See
above for their meanings. Read-only.
TracesStats tstats: A structure used by Traces to provide some statistics about
what it did. See above for their meanings. Write-only.
sparsegraph canong: The canonically labelled graph, if toptions.getcanon = TRUE.
Otherwise it can be NULL. Write-only.
25
Low level nauty calls
For most applications, the simplified interface to nauty described in the previous section
is recommended. This section describes the low-level interface used both for dense graphs
and sparse graphs. nauty knows which type you are using from the dispatch field of the
options argument.
A call to nauty has the form
nauty (g, lab, ptn, active, orbits, options, stats, workspace, worksize, m, n,
canong)
where the parameters have meanings as defined below.
graph or sparsegraph g: The input graph. Read-only. The actual parameter has type
graph, so your compiler might like you to cast a sparsegraph argument to that
type if you are using a sparse graph.
options. If options.defaultptn = TRUE, the input values are ignored; otherwise,
they define the initial colouring of the graph (see below). If options.getcanon =
TRUE, the value of lab on return is the canonical labelling of the graph. Precisely,
it lists the vertices of g in the order in which they need to be relabelled to give
canong. Irrespective of options.getcanon, neither lab nor ptn is changed by
enough to change the colouring. (Recall that the order of the vertices within the
cells is irrelevant.) Read-Write.
set active: An array of m setwords specifying the colours which are initially active.
A brief outline of what this means is given below. This argument is rarely used;
nauty will always work correctly if given the nil pointer NULL. Read-only.
int orbits: An array of n entries to hold the orbits of the automorphism group. When
nauty returns, orbits[i] is the number of the least-numbered vertex in the same
orbit as i, for 0 i n1. Write-only.
optionblk options: A structure giving a list of options to the procedure. See Section 5
for their meanings. Read-only.
statsblk stats: A structure used by nauty to provide some statistics about what it
did. See Section 5 for their meanings. Write-only.
setword workspace, worksize: The address and length of an array used by nauty for
working storage. The length is given in units of setword (differently from the w
command in dreadnaut). There is no minimum requirement for correct operation,
but the efficiency may suffer if not much is provided. A value of worksize 50m
is recommended. Write-only and read-only, respectively.
int m, n: The number of setwords in sets and the number of vertices, respectively.
It must be the case that 1 n m WORDSIZE. If nauty is compiled with
MAXN > 0, it must also be the case that n MAXN and m MAXM, where
MAXM = dMAXN/WORDSIZEe. Read-only.
graph or sparsegraph canong The canonically labelled isomorph of g produced by
26
nauty. This argument is ignored if options.getcanon = FALSE, in which case

the nil pointer NULL can be given as the actual parameter. Write-only. The type
must be the same as that of parameter g.
The C type of the parameters g and canong is graph. If another type of pointer is
passed (for example sparsegraph), it should be cast to type graph.
The initial colouring of the graph is determined by the values of the arrays lab, ptn
and the flag options.defaultptn. If options.defaultptn = TRUE, the contents of
lab and ptn are set by nauty so that every vertex has the same colour. If not, they are
assumed to have been set by the user. In this case, lab should contain a list of all the
vertices in some order such that vertices with the same colour are contiguous. The ends of
the colour-classes are indicated by zeros in ptn. In super-precise terms, each cell has the
form {lab[i], lab[i+1], . . . , lab[j]} where [i, j] is a maximal subinterval of [0, n1] such
that ptn[k] > 0 for i k < j and ptn[j] = 0. (In the terminology defined in Section 9,
this is the partition at level 0.) The order of the vertices within each cell has no effect
on the behaviour of nauty.
The concept of active cells is used by the procedure which implements the partition
refinement function R defined above. The details are given in [9], where the active cells
are in a sequence called . In this implementation, a set rather than a sequence is
used. If options.defaultptn = TRUE, or active = NULL, every colour is active.
This will always work, and so is recommended if you dont want to be a smart-arse. If
options.defaultptn = FALSE and active 6= NULL, the elements of active indicate
the indices (0 .. n1) where the active cells start in lab and ptn (see above). Theorem
2.7 of [9] gives some sufficient conditions for active to be valid. If these conditions are
not met, anything might happen. The most common places where this feature may save
a little time are:
(a) If the initial colouring is known to be already equitable, active can be the empty set.
(Dont confuse this with NULL, which causes nauty to set the active set to include
every cell.)
(b) If the graph is regular and the colouring has exactly two cells, active can indicate
just one of them (the smallest for best efficiency).
If nauty is used to test two graphs for isomorphism, it is essential that exactly the
same value of active be used for each of them.
Some of the fields in the options argument may change the canonical labelling
produced by nauty. These are fields digraph, defaultptn, tc level, userrefproc,
invarproc, mininvarlevel, maxinvarlevel, invararg and dispatch. The canonical
labelling also depends on whether the graph is in dense or sparse form. If nauty is used
to test two graphs for isomorphism, it is important that the same values of these options
be used for both graphs.
In addition to their parameters, the output routines of nauty respect the value of the
global int variable labelorg. If the value of labelorg is k, the output routines pretend
that the vertices of the graph are numbered k, k+1, . . . , n+k1, even though they are
27
always internally numbered 0, 1, . . . , n1. By default, k = 0. Only non-negative values

are supported.
8
8.1
Interpretation of the output

nauty output
If options.writeautoms = TRUE or options.writemarkers = TRUE, nauty writes

information concerning the automorphism group is written to the file options.outfile.
Let be the automorphism group, and let v1 ,v2 ,...,vi denote the point-wise stabiliser
in of v1 , v2 , . . . , vi . The output has the following general form:
(k)
1
(k)
2
.
.
.
(k)
tk
level k:
(k1)
1
(k1)
2
.
.
.
ck cells; rk orbits; vk fixed; index ik /jk
(k1)
tk1
level k1:
.
.
.
level 2:
(1)
1
(1)
2
.
.
.
ck1 cells; rk1 orbits; vk1 fixed; index ik1 /jk1

c2 cells; r2 orbits; v2 fixed; index i2 /j2
(1)
t1
level 1:
c1 cells; r1 orbits; v1 fixed; index i1 /j1
28
(j)
Here, v1 , v2 , . . . , vk is a sequence of vertices such that v1 ,v2 ,...,vk is trivial. The i

automorphisms. For 1 l k, the following are true.
(j)
(a) v1 ,v2 ,...,vl1 is generated by the automorphisms i
are
for l j k and 1 i tj .
(b) v1 ,v2 ,...,vl1 has rl orbits and order i1 i2 il .

(c) cl is the number of cells in the equitable partition at the ancestor at level l of the
first leaf of the tree, jl is the number of vertices in the target cell of the same node,
vl is the first vertex in that cell, and il is the number of vertices of that cell which are
equivalent to vl .
Pk
(d)
i=l ti n rl . This follows from the fact that the number of orbits of the group
generated by all the automorphisms found to up to any moment decreases as each new
automorphism is found. In particular, this means that the total number of generators
found is at most n1. Usually, it is much less.
The markers level... are only written if options.writemarkers = TRUE. In the
common circumstance that cl = rl , cl cells; is omitted. Similarly, /jl is omitted if
jl = il . Note that il = 1 is possible for more difficult graphs. Further information about
the generators can be found in Theorem 2.34 of [9].
Examples of nauty output
All of the following examples were run without the use of a vertex-invariant.
Example 1:
0
1
2
g =
4
7
options[getcanon = FALSE, digraph = FALSE, writeautoms = TRUE,

writemarkers = TRUE, defaultptn = TRUE, cartesian = FALSE, tc level = 0].
output:
(2 5)(3 4)
level 3:
6 orbits; 3 fixed; index 2
(1 3)(5 7)
level 2:
(0 1)(2 3)(4 5)(6 7)
level 1:
1 orbit; 0 fixed; index 8
orbits = (0,0,0,0,0,0,0,0), stats[grpsize1 = 48.0, grpsize2 = 0, numorbits = 1,
numgenerators = 3, numnodes = 10, numbadleaves = 0, maxlevel = 4].
Explanation of output: Let 1 , 2 and 3 be the three automorphisms found, in the order
29
written. Let be the automorphism group. Then

0,1,3
0,1
0
= {(1)}
= h1 i with 6 orbits and order 2
= h1 , 2 i with 4 orbits and order 2 3 = 6
= h1 , 2 , 3 i with 1 orbit and order 6 8 = 48.
The values of stats.grpsize1 and stats.grpsize2 show that | | = 48 100 = 48. The
value of stats.numorbits shows there is only one orbit, which is also seen from orbits.
Example 2:
0
1
2
g =
4
lab = (2,0,1,3,4,5,6,7), ptn = (0,1,1,1,1,1,1,0), active = NULL,

options[getcanon = FALSE, digraph = FALSE, writeautoms = TRUE,
writemarkers = TRUE, defaultptn = FALSE, cartesian = TRUE, tc level = 0].
output:
5 1 2 6 4 0 3 7
level 2:
0 3 2 1 4 7 6 5
level 1:
orbits = (0,1,2,1,4,0,1,0), stats[grpsize1 = 6.0, grpsize2 = 0, numorbits = 4,
numgenerators = 2, numnodes = 6, numbadleaves = 0, maxlevel = 3].
In this example we have set lab, ptn and options.defaultptn so that vertex 2 is
fixed. The automorphisms were written in the cartesian representation, which would
probably only be useful if they were going to be fed to another program. The value of
orbits on return indicates that the orbits of the group are {0, 5, 7}, {1, 3, 6}, {2} and {4}.
Example 3:
7
11
g =
0
10
options[getcanon = TRUE, digraph = FALSE, writeautoms = TRUE,

writemarkers = TRUE, defaultptn = TRUE, tc level = 0].
output:
(8 11)(9 10)
level 6:
(7 8)(9 11)
level 5:
(4 6)
30
level 4:
(3 4)(5 6)
level 3:
(1 2)
level 2:
(0 1)
level 1:

4 cells; 5 orbits; 3 fixed; index 4/9
3 cells; 4 orbits; 1 fixed; index 2
1 cell; 3 orbits; 0 fixed; index 3/12
orbits = (0,0,0,3,3,3,3,7,7,7,7,7), stats[grpsize1 = 480.0, grpsize2 = 0,

numorbits = 3, numgenerators = 6, numnodes = 40, numbadleaves = 2,
maxlevel = 7], lab = (3,4,6,5,7,8,11,9,10,0,1,2).
4
10
h =
9
11 1
6
7
Example 4:
11
3
4
g =
9
10
2
0
options[getcanon = TRUE, digraph = FALSE, writeautoms = FALSE,

writemarkers = FALSE, defaultptn = TRUE, tc level = 0].
No output written.
orbits = (0,0,0,0,0,5,5,5,5,9,9,9), stats[grpsize1 = 480.0, grpsize2 = 0,
numorbits = 3, numgenerators = 6, numnodes = 41, numbadleaves = 3,
maxlevel = 7], lab = (5,6,8,7,0,1,4,2,3,9,10,11).
1
11
h =
9
10
which is identical to the resulting canong in Example 3.
8.2
Traces output
Output from Traces is controlled by the writeautoms, cartesian, and verbosity options.
2
1
6
g =
5
0
31
toptions[getcanon = FALSE, writeautoms = TRUE,

defaultptn = TRUE, verbosity = 1].
output:
Gen #1:
Gen #2:
level 1:
Gen #3:
Gen #4:
Gen #5:
level 2:
level 3:
(0 4 3 7 5 1)(2 9 8)
(0 2)(3 4)(6 9)(7 8)
3 cells; target cell: 10; 1 orbit; 3 nodes (1 kept); 1 update;
(1 4 9)(2 8 7)(3 6 5)
(3 6)(4 9)(7 8)
(1 9 4)(2 6 8 5 7 3)
The lines starting Gen are generators for the group. Note that in Traces there is no
base and the generators do not in general form a strong generating set. The lines starting
level, which are turned on by the verbosity option, describe the levels in the search
tree:
(a) the level number (level 1 has the children of the root of the tree);
(b) the number of cells, and the size of the target cell, for the nodes on this level that
are the best;
(c) the number of orbits in the group generated by the generators found by the time this
level is finished;
(d) the number of nodes created on this level, and the number which are judged to be
best;
(e) the number of times a node was found on this level better than the previous nodes
on this level.
If known automorphisms are given to Traces via toptions.generators, these are
not written.
User-defined procedures
nauty makes provision for up to five procedures specified by the user to be called at
various times during the processing. This will be done if pointers to them are passed
in the userrefproc, userautomproc, usernodeproc, userlevelproc or usercanonproc
fields of options (see Section 7). In all cases, a value of NULL will cause no call to be
made.
Traces currently has two such procedures, userautomproc and usercanonproc.
Proceedures for nauty.
These procedures have many parameters in common; we will describe the most important of these here. Unless the individual procedure descriptions specify otherwise, they
should be treated as read-only.
graph g; int m, n: These are the arguments of the same name passed to nauty. nauty
has not changed them. See Section 7 for their meanings. If the sparse version
32
of nauty is being used, the argument passed to parameter g actually has type
sparsegraph*. Correct practice is declare it as type graph* but cast it to type
sparsegraph* before use.
int level: The level of the current node. The root of the search tree has level one.
int lab, ptn: Arrays of length n giving partitions associated with each of the nodes
along the path from the root of the tree to the current node. These are the parameters of the same name passed to nauty, but nauty has modified their contents as
described below.
Suppose that we are currently at level l of the search tree. Let 1 , 2 , . . . , l be the
path in the tree from the root 1 to the current node l . The partition at level i is a
partition i associated with node i . The partition originally passed to nauty, implicitly
or explicitly, is the partition at level 0, denoted by 0 . The complete partition nest
0 , 1 , . . . , l is held in lab and ptn thus:
(a) lab holds a permutation of {0, 1, . . . , n1}.
(b) For 0 t l, the partition t has as cells all the sets of the form {lab[i], lab[i+1],
. . . , lab[j]}, where [i, j] is a maximal subinterval of [0, n1] such that ptn[k] > t for
i k < j and ptn[j] t.
(c) Every entry of ptn which is not less than or equal to l is equal to NAUTY INFINITY.
(NAUTY INFINITY is a large constant defined in nauty.h.)
For example, say n = 10, l = 3, 0 = [0, 2, 4, 5, 6, 7, 8, 9|1, 3], 1 = [0, 2, 4, 6|5, 7, 8, 9|1, 3],
2 = [0, 2, 4, 6|8|5, 7, 9|3|1], and 3 = [4, 6|0, 2|8|5, 7, 9|3|1]. Then the contents of lab and
ptn may be
lab: 4 6 2 0 8 7
ptn: 3 1 2
5 9 3 1
0 2 0
The order of the vertices within the cells of l is arbitrary.

We will refer to the partition at level l as the current partition.
(a) userrefproc(g, lab, ptn, level, numcells, count, active, code, m, n)
This is a procedure to replace the default partition-refinement procedure, and is called
for each node of the tree. The partition associated with the node is the partition at level
level, which is defined above.
The parameters passed are as follows.
g,m,n,lab,ptn,level: As above. The parameters lab and ptn may be altered by this
procedure to the extent of making the current partition finer. The partitions at
higher levels must not be altered.
int numcells: The number of cells in the current partition. This must be updated if
the number of cells is increased.
int count: This is the address of an array of length at least n which can be used as
scratch space. It can be changed at will.
set active: The set of active cells. This is not the same as the parameter of the same
33
name passed to nauty, but has the same meaning and purpose. It can be changed
without affecting nauty behaviour. See Section 7.
int code: This must be set to a labelling-independent value which is an invariant of the
partition at this level before or after refinement. (Example: the number of cells.)
It is essential that equivalent nodes have the same code. The value assigned must
be less than NAUTY INFINITY.
The operation of refining the current partition involves permuting the vertices (i.e.,
entries of lab) within a cell, and then breaking it into subcells by changing the appropriate
entries of ptn to level.
The validity of nauty requires that the operation performed be entirely independent
of the labelling of the graph. Thus, if userrefproc is called with g and lab relabelled
consistently and the same values of ptn and active, then the final values of ptn and
active should be the same, and the final value of lab should be the same but relabelled
in the same way (remembering always that the order of vertices within the cells doesnt
matter). It is also necessary that nodes of the tree which may be equivalent must be
treated equivalently. To be safe, regard any nodes on the same level as possibly equivalent.
It is desirable (but not compulsory) that the partition returned is equitable. If necessary, this can be done by calling the default refinement procedure refine, which has the
same parameter list. If equitablility cannot be ensured, make sure that nauty is called
with options.digraph = TRUE.
The usefulness of userrefproc has declined since vertex-invariants were introduced
(see Section 10).
(b) usernodeproc(g, lab, ptn, level, numcells, tc, code, m, n)
This is called once for every node of the search tree, after the partition has been
refined.
The parameters passed are as follows. Treat all of them as read-only.
g,m,n,lab,ptn,level: As above.
int numcells: The number of cells in the current partition.
int tc: If nauty has determined that children of this node need to be explored, tc is
the index in lab of where the target cell starts. Otherwise, it is 1.
int code: This is the code produced by the refinement and vertex-invariant procedures
while refining this partition.
34
(c) userautomproc(count, perm, orbits, numorbits, stabvertex, n)

This is called once for each generator of the automorphism group, in the same order
as they are written (see Section 8). It is provided to facilitate such tasks as storing the
generators for later use, writing them in some unusual manner, or converting them into
another representation (for example, into their actions on the edges).
(j)
Suppose the generator is = i , in the notation of Section 8. Then the parameters

have meanings as below. Treat them all as read-only.
int count: The ordinal of this generator. The first is number 1.
int perm: The generator itself. For 0 i < n, perm[i] = i .
int orbits; int numorbits: The orbits and number of orbits of the group generated
by all the generators found so far, including this one. See Section 7 for the format
of orbits.
int stabvertex: The value vj , as defined in Section 8.
int n: The number of vertices, as usual.
(d) userlevelproc(lab, ptn, level, orbits, stats, tv, index, tcellsize, numcells,
childcount, n)
This is called once for each node on the leftmost path downwards from the root, in
bottom to top order. It corresponds to the markers level ..., which are described
in Section 8, except that an additional, initial, call is made for the first leaf of the tree.
The purpose is to provide more information than is provided by the markers, in a manner
which enables it to be stored for later use, etc.. The parameters passed are as follows.
Treat them all as read-only.
n,lab,ptn,level: As above. The values of level will decrease by one for each call,
reaching one for the final call.
Suppose that the value of level is l.
int orbits: The orbits of the group generated by all the automorphisms found so far.
See Section 7 for the format. In the notation of Section 8, orbits gives the orbits
of the stabiliser v1 ,v2 ,...,vl1 .
statsblk stats: The meaning is as given in Section 7, except that it applies to the
group generated by all the automorphisms found so far, that is to v1 ,v2 ,...,vl1 . Only
the fields which refer to the group can be assumed correct.
int tv, index, tcellsize, numcells: In the notation of Section 8, these are the values
of vl , il , jl and cl , respectively. For the first call, their values are 0, 1, 1 and n,
respectively.
int childcount: This is the number of children of the node at level level on the first
path down the tree which were actually generated.
The condition numcells = n can be used to identify the first call.
35
(e) int usercanonproc(g, lab, canong, count, code, m, n)

Provided options.getcanon=TRUE, this procedure is called whenever nauty updates its best-so-far labelling.
If the value returned by the procedure is 0, there will be no effect on the behaviour
of nauty. If the value returned is 1, nauty will immediately return to the program that
called it without any further processing. In that case the errstatus field of the stats
argument to nauty will be set to the value NAUABORTED, but otherwise no fields in
stats will have meaningful values.
Return values other than 0 and 1 are reserved for future enhancements.
The parameters passed are as follows. Treat all of them as read-only.
g,m,n,lab: As above.
graph canong: The best labelling so far. That is, canong is g with its vertices relabelled
in the order given by lab.
int count: The ordinal of this labelling. The first is 1, corresponding to the first leaf of
the search tree.
int code: This is the code produced by the refinement and vertex-invariant procedures
while refining this partition. It is an invariant of canong coloured in the same way
as the input graph.
Proceedures for Traces.
(a) userautomproc(count, perm, n)
This is called once for each generator of the automorphism group, in the same order as
they are written. It is provided to facilitate such tasks as storing the generators for later
use, writing them in some unusual manner, or converting them into another representation
(for example, into their actions on the edges).
The parameters have meanings as below. Treat them all as read-only.
int count: The ordinal of this generator. The first is number 1.
int perm: The generator itself. For 0 i < n, perm[i] = i .
int n: The number of vertices, as usual.
(b) int usercanonproc(g, lab, canong, count, code, m, n)
This behaves the same as in nauty, see the description above.
36
10
Vertex-invariants
The operation of nauty and Traces is driven by a procedure which accepts partitions
and attempts to make them strictly finer without separating equivalent vertices. For some
families of difficult graphs, the built-in refinement procedure is insufficiently powerful,
resulting in excessively large search trees. In many cases, this problem can be dramatically
reduced by using some sort of invariant to assist the refinement procedure.
Traces does not have the facility to use invariants during its operation, though dreadnaut allows an invariant to be applied before Traces is called.
Formally, let G be the set of all labelled graphs (or digraphs) with vertex set V =
{0, 1, . . . , n1}, and let be the set of partitions of V . As always, the order of the cells
of a partition is significant, but the order of the elements of the cells is not. Let Z be the
integers. A vertex-invariant is defined to be a mapping
: G V Z
such that (G , , v ) = (G, , v) for every G G, , v V and permutation .
Informally, this says that the values of are independent of the labelling of G.
A great number of vertex-invariants have been proposed in the literature, but very few
of them are suitable for use with nauty. Most of them are either insufficiently powerful
or require excessive amounts of time or space to compute. Even amongst the vertexinvariants which are known to be useful, their usefulness varies so much with the type
of graph they are applied to, or the levels of the search tree at which they are applied,
that intelligent automatic selection of a vertex-invariant by nauty would seem to be a
task beyond our current capabilities. Consequently, the choice of vertex-invariant (or the
choice not to use one) has been left up to the user.
The options parameter of nauty has four fields relevant to vertex-invariants, namely
invarproc, mininvarlevel, maxinvarlevel and invararg. These are fully described in
Section 7. The I command in dreadnaut may be useful in investigating which of the
supplied vertex-invariants are useful for your problem. Experience shows that it is nearly
always best to apply the invariant at just one level in the search tree, with levels 1 and 2
being the most likely candidates.
We now describe the vertex-invariants which are provided with nauty. Information
on how to write a new vertex-invariant procedure can be found in the file nautinv.c. We
will assume that g is a graph on V = {0, 1, . . . , n1}, and that = (V0 , V1 , . . . , Vk ) is a
partition of V . This partition will be equitable unless options.digraph = TRUE. One of
the cells of will be designated V . If the procedure is called by nauty at level 1 (i.e.
at the root of the search tree), or directly by dreadnaut (I command), this will be the
first cell V0 ; otherwise, V will be the singleton cell containing the vertex fixed in order
to create this node from its parent.
Unless otherwise specified, these invariants are only available for graphs in dense form.
Trying to use them with sparse form will cause a disaster.
twopaths.
Each vertex v is given a code depending on the cells to which belong the
vertices reachable from v along a path of length 2. invararg is not used. This is a cheap
37
invariant suitable for graphs which are regular but otherwise have no particular structure
(for example).
adjtriang. Each vertex v is given a code depending on the number of common neighbours between each pair {v1 , v2 } of neighbours of v, and which cells v1 and v2 belong to.
v1 must be adjacent to v2 if invararg = 0 and not adjacent if invararg = 1 . This is a
fairly cheap invariant which can often break up the vertex sets of strongly-regular graphs.
triples.
Each vertex v is given a code depending on the set of weights w(v, v1 , v2 ),
where {v1 , v2 } ranges over the set of all pairs of vertices distinct from v such that at
least one of {v, v1 , v2 } lies in V . The weight w(v, v1 , v2 ) depends on the number of
vertices adjacent to an odd number of {v, v1 , v2 } and to the cells that v, v1 and v2 belong
to. invararg is not used. This invariant often works on strongly-regular graphs that
adjtriang fails on, but is more expensive.
quadruples. Each vertex v is given a code depending on the set of weights w(v, v1 , v2 , v3 ),
where {v1 , v2 , v3 } ranges over the set of all pairs of vertices distinct from v such that at
least one of {v, v1 , v2 , v3 } lies in V . The weight w(v, v1 , v2 , v3 ) depends on the number of
vertices adjacent to an odd number of {v, v1 , v2 , v3 } and to the cells that v, v1 , v2 and v3
belong to. invararg is not used. This is an expensive invariant which can sometimes be
of use for graphs with a particularly regular structure.
celltrips. Each vertex v is given a code depending on the set of weights w(v, v1 , v2 ),
where w(v, v1 , v2 ) depends on the number of vertices adjacent to an odd number of
{v, v1 , v2 }. These three vertices are constrained to belong to the same cell. The cells
of are tried in increasing order of size until one splits. invararg is not used. This
invariant can sometimes split the bipartite graphs derived from block designs, and other
graphs of moderate difficulty.
cellquads. Each vertex v is given a code depending on the set of weights w(v, v1 , v2 , v3 ),
where w(v, v1 , v2 , v3 ) depends on the number of vertices adjacent to an odd number of
{v, v1 , v2 , v3 }. These four vertices are constrained to belong to the same cell. The cells of
are tried in increasing order of size until one splits. invararg is not used. This invariant
is powerful enough to split many difficult graphs, such as hadamard-matrix graphs (where
it is best applied at level 2).
cellquins. Each vertex v is given a code depending on the set of weights
w(v, v1 , v2 , v3 , v4 ), where w(v, v1 , v2 , v3 , v4 ) depends on the number of vertices adjacent to
an odd number of {v, v1 , v2 , v3 , v4 }. These five vertices are constrained to belong to the
same cell. The cells of are tried in increasing order of size until one splits. invararg is
not used. We know of no good use for this very powerful but very expensive invariant.
distances. Each vertex v is given a code depending on the number of vertices at each
distance from v, and what cells they belong to. If a cell is found that splits, no further
cells are tried. invararg specifies an upper bound on which distance to investigate, with
0 indicating no limit. This is a fairly cheap invariant suitable for things like regular
graphs for which twopaths doesnt work. Use the smallest value of invararg that gives
satisfactory results.
This is like distances but works for sparse form rather than dense
distances sg.
form. It is in the file nausparse.c rather than nautyinv.c.
38
indsets. Each vertex v is given a code depending on the number of independent sets
of size invararg which include v, and the cells containing the other vertices of those sets.
The value of invararg is limited to 10. This can often split the vertex sets of stronglyregular graphs and bipartite design graphs, though it becomes expensive if invararg is
large. A value of 4 is sometimes sufficient.
cliques.
Each vertex v is given a code depending on the number of cliques of size
invararg which include v, and the cells containing the other vertices of those cliques. The
value of invararg is limited to 10. This can often split the vertex sets of strongly-regular
graphs, though it becomes expensive if invararg is large. A value of 4 is sometimes
sufficient.
cellcliq.
Each vertex v is given a code depending on the number of cliques of size
invararg which include v and lie within the cell containing v. The value of invararg is
limited to 10. The cells are tried in increasing order of size, and the process stops as soon
as a cell splits. This invariant applied at level 2 can be very successful on difficult vertextransitive graphs. A value of 3 can sometimes work even on strongly-regular graphs.
cellind.
Each vertex v is given a code depending on the number of independent
sets of size invararg which include v and lie within the cell containing v. The value of
invararg is limited to 10. The cells are tried in increasing order of size, and the process
stops as soon as a cell splits. This invariant applied at level 2 can be very successful on
difficult vertex-transitive graphs.
adjacencies. This is an invariant for digraphs and is not useful for graphs. The standard refinement procedure alone can sometimes give very poor performance for directed
graphs, especially those which are not strongly connected. This invariant tries to correct
the poor behaviour. Applying it to multiple levels may be necessary.
This is like adjacencies but works for sparse form rather than
adjacencies sg.
dense form. It is in the file nausparse.c rather than nautyinv.c.
cellfano.
This invariant is intended for projective plane graphs but can be applied
to any graphs. It is very expensive.
cellfano2.
This invariant is intended for projective plane graphs but can be applied
to any graphs. It is very expensive, but maybe less than cellfano for genuine projective
plane graphs. In the latter case, it can be thought of as counting the Fano subplanes
according to which cells they involve. Another class of graph that this invariant can help
with is the graphs derived from Latin squares as in Section 14.
refinvar.
Each vertex is given a code that depends on the result of refining the
partition resulting from individualization of that vertex. The refinement is not necessarily
complete; its completeness depends on the value of invararg. Use the smallest value of
invararg that gives satisfactory results. This is good for regular graphs that are not
strongly regular, and similar graphs.
39
11
Writing programs which call dense nauty
Programs which call the dense version of nauty should include the file nauty.h and be
linked with nauty.c, nautil.c, naugraph.c, schreier.c, and naurng.c. If a built-in
invariant is used, the file nautinv.h should be included too, and nautinv.c should be
linked.
The simplest way to link with the necessary object files is to use the library nauty.a.
Suppose that m and n have meanings as usual.
There are two general approaches to storage management. The first, the simplest if a
prior limit is known on the graph size, is to define MAXN to be that limit before nauty.h
is included. nauty.h will define MAXM, and then MAXM and MAXN can be used to
declare variables. For example:
set s[MAXM]; /* a set */
graph g[MAXN*MAXM]; /* a graph */
int xy[MAXN]; /* an array */
The second method is more complicated but does not require a prior bound on the
graph size. In this method, each variable whose size is unknown is dynamically allocated.
Of course you can do this yourself using malloc( ) but nauty.h provides macros for doing
it in a convenient and efficient way. First there are static declarations:
DYNALLSTAT(set,s,s sz);
DYNALLSTAT(graph,g,g sz);
DYNALLSTAT(int,xy,xy sz);
Before the variables are used, they are set to the right size using the dynamic allocation
macros:
DYNALLOC1(set,s,s sz,m,"malloc");
DYNALLOC2(graph,g,g sz,m,n,"malloc");
DYNALLOC1(int,xy,xy sz,n,"malloc");
To take the first variable as an example, the result of the macro will be that s has
a value of type set which points to an array of length at least m. If DYNALLOC1 or
DYNALLOC2 is used again for the same variable, it is freed and allocated again only
if the new requested size is larger than the previous size. Otherwise the same space is
reused. This is intended to be more efficient that repeated unnecessary calls to malloc( )
and free( ). In case it is desired to free the object allocated by DYNALLOC1, use, for
example, DYNFREE(s,s sz). There is also CONDYNFREE that frees objects if they are
bigger than a given size.
In the case of g, we used DYNALLOC2 instead of DYNALLOC1. This is slightly
better as it covers the possibility that mn is too large for an int. We could also use
DYNALLOC1(graph,g,g sz,m*(size t)n,"malloc");
The last parameter of DYNALLOC1 and DYNALLOC2 is a string used in an error
message in the event that the allocation fails.
nauty.h also defines a number of macros that are useful for programming with the
40
nauty data structures. Some of the more useful macros are as follows.
SETWORDSNEEDED(n) : the least number of setwords needed for n bits.
ADDELEMENT(s,i) : add element i to set s.
DELELEMENT(s,i) : delete element i from set s.
FLIPELEMENT(s,i) : delete element i from set s if it is present, or insert it if it is
absent.
ISELEMENT(s,i) : test if i is an element of the set s (0 i n1).
EMPTYSET(s,m) : make the set s equal to the empty set.
POPCOUNT(x) : the number of 1-bits in the setword x.
Use ((x)?POPCOUNT(x):0) in circumstances where x is most often zero. Note that
the fastest version of this macro may need a compiler switch: see the value of
CFLAGS in makefile after configuration.
FIRSTBIT(x) : the position (0 to WORDSIZE 1) of the first (least-numbered) 1-bit in
the setword x, or WORDSIZE if there is none.
FIRSTBITNZ(x) : This is a faster version of FIRSTBIT, but it assumes that x 6= 0.
TAKEBIT(i,x) : If the setword x is not 0, set i to the position (0 to WORDSIZE 1)
of the first (least-numbered) 1-bit in x, and remove that bit from x.
ALLBITS : A setword constant with the first WORDSIZE bits set (this is usually all
the bits).
BITMASK(i) : A setword constant with the first i + 1 bits unset and the other
WORDSIZE i 1 numbered bits set, for 0 i < WORDSIZE. Thus, ANDing a
setword with BITMASK(i) deletes bits 0..i.
ALLMASK(i) : A setword constant with the first i bits set and all other bits unset, for
0 i WORDSIZE.
GRAPHROW(g,v,m) : The address of the row of graph g corresponding to the neighbours
of vertex v.
EMPTYGRAPH(g,m,n) : Makes a graph empty (i.e., no edges).
ADDONEARC(g,v,w,m) : Add one directed edge to a graph.
ADDONEEDGE(g,v,w,m) : Add one undirected edge to a graph.
SETWORD SHORT, SETWORD INT, SETWORD LONG, SETWORD LONGLONG :
Exactly one of these is defined, according to which unsigned integer type is the same
as setword.
SETWORDSNEEDED(n) : Calculates dn/WORDSIZEe, the number of setwords needed
to hold a subset of {0, 1, . . . , n1}.
SETWORD FORMAT : A string suitable for writing a value of type setword with
fprintf. For example it might be "%08lx".
41
Some of the procedures in nautil.c or naugraph.c may be useful. They are declared
in nauty.h. See the source code for the parameter list and semantics of these:
nextelement : find the position of the next element in a set following a specified position.
The recommended way to do something for each element of the set s is like this:
for (i = -1; (i = nextelement(s,m,i)) >= 0;)
{Process element i }
If you just want to do something for each bit in a setword x, it is more efficient to
do it like this:
tmp = x;
while (tmp)
{
TAKEBIT(i,tmp);
Process element i;
}
permset : apply a permutation to a set.
orbjoin : update the orbits of a group according to a new generator.
writeperm : write a permutation to a file.
isautom : test if a permutation is an automorphism.
updatecan : (for samerows = 0) relabel a graph.
refine : find coarsest equitable partition not coarser than given partition.
refine1 : produces exactly the same results as refine, but assumes m = 1 for greater
speed.
The file naututil.c contains procedures which are used by the dreadnaut program
(see Section 2). Many of these are also useful to programs which call nauty. If your
program uses them, include naututil.h as well as nauty.h.
Some of the more useful procedures are:
setsize : find cardinality of set.
setinter : find cardinality of intersection of two sets.
putset : write a set to a file.
putgraph : write a graph to a file.
putorbits : write a set of orbits to a file.
putptn : write a partition to a file.
readgraph : read a graph from a file.
readptn : read a partition from a file.
ranperm : generate a random permutation.
rangraph : generate a random graph.
42
complement : take the complement of a graph.

converse : take the converse of a digraph.
cellstarts : find the places where the cells at a given level begin.
sublabel : extract an induced subgraph of a graph.
In addition, the files nautaux.c, gutil1.c and gutil2.c contain a few procedures
which manipulate graphs or partitions, or compute properties of them, but which are not
currently used by nauty, Traces or dreadnaut.
It is recommended that programs which call nauty use the call
nauty check(WORDSIZE,m,n,NAUTYVERSIONID);
which will verify that a compatible verion of nauty is being used. This only needs to be
done once.
We next give some programs which illustrate simple use of dense nauty. The source
files are included in the nauty distribution.
43
11.1
nautyex1.c : Dense form with static allocation
/* This program prints generators for the automorphism group of an

n-vertex polygon, where n is a number supplied by the user.
This version uses a fixed limit for MAXN.
*/
#define MAXN 1000
#include "nauty.h"
/* Define this before including nauty.h */

/* which includes <stdio.h> and other system files */
int
main(int argc, char *argv[])
{
graph g[MAXN*MAXM];
int lab[MAXN],ptn[MAXN],orbits[MAXN];
static DEFAULTOPTIONS_GRAPH(options);
statsblk stats;
int n,m,v;
/* Default options are set by the DEFAULTOPTIONS_GRAPH macro above.
Here we change those options that we want to be different from the
defaults. writeautoms=TRUE causes automorphisms to be written.
*/
options.writeautoms = TRUE;
while (1)
{
printf("\nenter n : ");
if (scanf("%d",&n) != 1 || n <= 0)
break;
/* Exit if EOF or bad number */
if (n > MAXN)
{
printf("n must be in the range 1..%d\n",MAXN);
exit(1);
}
/* The nauty parameter m is a value such that an array of
m setwords is sufficient to hold n bits. The type setword
is defined in nauty.h. The number of bits in a setword is
WORDSIZE, which is 16, 32 or 64. Here we calculate
m = ceiling(n/WORDSIZE).
*/
m = SETWORDSNEEDED(n);
44
/* The following optional call verifies that we are linking

to compatible versions of the nauty routines.
*/
nauty_check(WORDSIZE,m,n,NAUTYVERSIONID);
/* Now we create the cycle. First we zero the graph, than for
each v, we add the edge (v,v+1), where values are mod n. */
EMPTYGRAPH(g,m,n);
for (v = 0; v < n; ++v)
ADDONEEDGE(g,v,(v+1)%n,m);
printf("Generators for Aut(C[%d]):\n",n);

/* Since we are not requiring a canonical labelling, the last
parameter to densenauty() is not required and can be NULL. */
densenauty(g,lab,ptn,orbits,&options,&stats,m,n,NULL);
/* The size of the group is returned in stats.grpsize1 and
stats.grpsize2. */
printf("Automorphism group size = ");
writegroupsize(stdout,stats.grpsize1,stats.grpsize2);
printf("\n");
}
exit(0);
}
45
11.2
nautyex2.c : Dense form with dynamic allocation

This version uses dynamic allocation.
*/
#include "nauty.h"
/* MAXN=0 is defined by nauty.h, which implies dynamic allocation */
int
{
/* DYNALLSTAT declares a pointer variable (to hold an array when it
is allocated) and a size variable to remember how big the array is.
Nothing is allocated yet. */
DYNALLSTAT(graph,g,g_sz);
DYNALLSTAT(int,lab,lab_sz);
DYNALLSTAT(int,ptn,ptn_sz);
DYNALLSTAT(int,orbits,orbits_sz);
statsblk stats;
int n,m,v;
set *gv;
/* Default options are set by the DEFAULTOPTIONS_GRAPH macro above.
Here we change those options that we want to be different from the
defaults. writeautoms=TRUE causes automorphisms to be written. */
while (1)
{
if (scanf("%d",&n) == 1 && n > 0)
{
/* The nauty parameter m is a value such that an array of
m setwords is sufficient to hold n bits. The type setword
is defined in nauty.h. The number of bits in a setword is
WORDSIZE, which is 16, 32 or 64. Here we calculate
m = ceiling(n/WORDSIZE). */
46
/* The following optional call verifies that we are linking

to compatible versions of the nauty routines. */
/* Now that we know how big the graph will be, we allocate
* space for the graph and the other arrays we need. */
DYNALLOC2(graph,g,g_sz,m,n,"malloc");
DYNALLOC1(int,lab,lab_sz,n,"malloc");
DYNALLOC1(int,ptn,ptn_sz,n,"malloc");
DYNALLOC1(int,orbits,orbits_sz,n,"malloc");
EMPTYGRAPH(g,m,n);
for (v = 0; v < n; ++v) ADDONEEDGE(g,v,(v+1)%n,m);
printf("order = ");
printf("\n");
}
else
break;
}
exit(0);
}
47
11.3
nautyex8.c : Determining an isomorphism, dense form

4
0
1
9
5
2
9
4
6
0
Figure 2: Two labellings of a Moebius graph.
/* This program demonstrates how an isomorphism is found between

two graphs, using the Moebius graphs as an example.
This version uses dense form with dynamic allocation.
*/
#include "nauty.h"
int
{
DYNALLSTAT(int,lab1,lab1_sz);
DYNALLSTAT(int,map,map_sz);
DYNALLSTAT(graph,g1,g1_sz);
DYNALLSTAT(graph,g2,g2_sz);
DYNALLSTAT(graph,cg1,cg1_sz);
DYNALLSTAT(graph,cg2,cg2_sz);
statsblk stats;
int n,m,i;
size_t k;
/* Select option for canonical labelling */
options.getcanon = TRUE;
while (1)
{
48
if (scanf("%d",&n) == 1 && n > 0)
{
if (n%2 != 0)
{
fprintf(stderr,"Sorry, n must be even\n");
continue;
}
DYNALLOC1(int,lab1,lab1_sz,n,"malloc");
DYNALLOC1(int,map,map_sz,n,"malloc");
/* Now make the first graph */
DYNALLOC2(graph,g1,g1_sz,n,m,"malloc");
EMPTYGRAPH(g1,m,n);
for (i = 0; i < n; i += 2)
ADDONEEDGE(g1,i,i+1,m);
/* Spokes */
for (i = 0; i < n-2; ++i) /* Cycle */

ADDONEEDGE(g1,i,i+2,m);
ADDONEEDGE(g1,1,n-2,m);
ADDONEEDGE(g1,0,n-1,m);
/* Now make the second graph */
DYNALLOC2(graph,g2,g2_sz,n,m,"malloc");
EMPTYGRAPH(g2,m,n);
for (i = 0; i < n; ++i)
{
ADDONEEDGE(g2,i,(i+1)%n,m);
/* Rim */
ADDONEEDGE(g2,i,(i+n/2)%n,m); /* Diagonals */
}
/* Create canonical graphs */
DYNALLOC2(graph,cg1,cg1_sz,n,m,"malloc");
DYNALLOC2(graph,cg2,cg2_sz,n,m,"malloc");
densenauty(g1,lab1,ptn,orbits,&options,&stats,m,n,cg1);
49
densenauty(g2,lab2,ptn,orbits,&options,&stats,m,n,cg2);
/* Compare canonically labelled graphs */
for (k = 0; k < m*(size_t)n; ++k)
if (cg1[k] != cg2[k]) break;
if (k == m*(size_t)n)
{
printf("Isomorphic.\n");
if (n <= 1000)
{
/* Write the isomorphism. For each i, vertex lab1[i]
of sg1 maps onto vertex lab2[i] of sg2. We compute
the map in order of labelling because it looks better. */
for (i = 0; i < n; ++i) map[lab1[i]] = lab2[i];
for (i = 0; i < n; ++i) printf(" %d-%d",i,map[i]);
printf("\n");
}
}
else
printf("Not isomorphic.\n");
}
else
break;
}
exit(0);
}
12
Writing programs which call sparse nauty
The basic data structure for sparse representation is the structure sparsegraph defined in Section 3. Programs using it should include nausparse.h and link with the
file nausparse.c.
As described in Section 3, the sparse representation of a graph uses a structure of type
sparsegraph with the following fields:
int nv: the number of vertices
int nde: the number of directed edges (loops count as 1)
int v: pointer to an array of length at least nv
int d: pointer to an array of length at least nv
int e: pointer to an array of length at least nde
50
sg weight w: not implemented in this version, should be NULL

size t vlen, dlen, elen, wlen: the actual lengths of the arrays v, d, e and w. The unit
is the element type of the array in each case (so vlen is the number of ints in the
array v, etc.)
For definiteness we will assume that such a graph is declared thus:
sparsegraph sg;
Before use this should be initialised, for which there is a macro:
SG INIT(sg);
or alternatively you can declare and initialise it at once:
SG DECL(sg);
To allocate the v, d and e arrays for a graph with n vertices and e directed edges, use
SG ALLOC(sg,n,e,"message");
where the message is used if allocation fails, and to free this space use
SG FREE(sg);
A particular graph can be stored in several different ways, since the lists of neighbours
of vertex do not need to be contiguous in sg.e, nor do they need to be sorted. However,
they are not allowed to overlap. To tell if two sparse graphs are identical, there is a
procedure aresame sg in nausparse.c.
The canonically labelled graph produced by nauty or Traces is guaranteed to have
contiguous adjacency lists but they are not necessarily sorted. It also has a specific value
of sg.v[i] if vertex i has degree 0, namely 0 for i = 0 and sg.v[i1]+1 otherwise. If
you plan to write the canonical graph using writes6 sg, you should sort it first using
sortlists sg. Sorting is not needed if you plan to write using writeg6 sg or writed6 sg.
Some utilities for handling sparse form graphs can be found in nausparse.c:
aresame sg : Test if two sparse graphs are the same. (Note: this is not an isomorphism
test, just a labelled graph comparison.)
sortlists sg : Sort the neighbourhood lists sg.e[sg.v[i] .. sg.v[i]+sg.v[i]-1] into ascending order.
put sg : Write a sparse graph in human-readable format.
copy sg : Make a copy of a sparse graph.
sg to nauty : Convert sparse form to dense form.
nauty to sg : Convert dense form to sparse form.
Now we give versions of the previous two programs that use sparse nauty instead of
dense nauty.
51
12.1
nautyex4.c : Sparse form with dynamic allocation

This version uses sparse form with dynamic allocation.
*/
#include "nausparse.h"
/* which includes nauty.h */
int
{
static DEFAULTOPTIONS_SPARSEGRAPH(options);
statsblk stats;
sparsegraph sg;
/* Declare sparse graph structure */
int n,m,i;
/* Initialise sparse graph structure. */
SG_INIT(sg);
while (1)
{
if (scanf("%d",&n) == 1 && n > 0)
{
/* SG_ALLOC makes sure that the v,d,e fields of a sparse graph
structure point to arrays that are large enough. This only
works if the structure has been initialised. */
SG_ALLOC(sg,n,2*n,"malloc");
sg.nv = n;
sg.nde = 2*n;
/* Number of vertices */
/* Number of directed edges */
52
for (i = 0; i < n; ++i)

{
sg.v[i] = 2*i;
sg.d[i] = 2;
sg.e[2*i] = (i+n-1)%n;
sg.e[2*i+1] = (i+n+1)%n;
}
/* edge i->i-1 */
/* edge i->i+1 */

sparsenauty(&sg,lab,ptn,orbits,&options,&stats,NULL);
printf("\n");
}
else
break;
}
exit(0);
}
53
12.2
nautyex5.c : Sparse form with dynamic allocation

two graphs, using the Moebius graph as an example.
This version uses sparse form with dynamic allocation.
*/
#include "nausparse.h"
/* which includes nauty.h */
int
{
static DEFAULTOPTIONS_SPARSEGRAPH(options);
statsblk stats;
/* Declare and initialize sparse graph structures */
SG_DECL(sg1); SG_DECL(sg2);
SG_DECL(cg1); SG_DECL(cg2);
int n,m,i;
/* Read the number of vertices and process it */
while (1)
{
if (scanf("%d",&n) == 1 && n > 0)
{
if (n%2 != 0)
{
continue;
}
54
SG_ALLOC(sg1,n,3*n,"malloc");
sg1.nv = n;
sg1.nde = 3*n;
for (i = 0; i < n; ++i)
{
sg1.v[i] = 3*i;
/* Position of vertex i in v array */
sg1.d[i] = 3;
/* Degree of vertex i */
}
for (i = 0; i < n; i += 2)
{
sg1.e[sg1.v[i]] = i+1;
sg1.e[sg1.v[i+1]] = i;
}
/* Spokes */
for (i = 0; i < n-2; ++i) /* Clockwise edges */

sg1.e[sg1.v[i]+1] = i+2;
sg1.e[sg1.v[n-2]+1] = 1;
sg1.e[sg1.v[n-1]+1] = 0;
for (i = 2; i < n; ++i) /* Anticlockwise edges */
sg1.e[sg1.v[i]+2] = i-2;
sg1.e[sg1.v[1]+2] = n-2;
sg1.e[sg1.v[0]+2] = n-1;
sg2.nv = n;
sg2.nde = 3*n;
for (i = 0; i < n; ++i)
{
sg2.v[i] = 3*i;
sg2.d[i] = 3;
}
for (i = 0; i < n; ++i)
{
sg2.v[i] = 3*i;
sg2.d[i] = 3;
sg2.e[sg2.v[i]] = (i+1) % n;
55
/* Clockwise */
sg2.e[sg2.v[i]+1] = (i+n-1) % n;
sg2.e[sg2.v[i]+2] = (i+n/2) % n;
/* Anti-clockwise */
/* Diagonals */
}
/* Label sg1, result in cg1 and labelling in lab1; similarly sg2.
It is not necessary to pre-allocate space in cg1 and cg2, but
they have to be initialised as we did above. */
sparsenauty(&sg1,lab1,ptn,orbits,&options,&stats,&cg1);
sparsenauty(&sg2,lab2,ptn,orbits,&options,&stats,&cg2);
if (aresame_sg(&cg1,&cg2))
{
if (n <= 1000)
{
printf("\n");
}
}
else
}
else
break;
}
exit(0);
}
13
Writing programs which call Traces
Traces uses the same data structures for graphs, partitions, permutations and orbits as
sparse nauty, so the functions for manipulating sparse graphs can be used unchanged.
Here we give the previous program again, using Traces.
56
13.1
nautyex7.c : Determining an isomorphism using Traces

This version uses Traces.
*/
#include "traces.h"
int
{
static DEFAULTOPTIONS_TRACES(options);
TracesStats stats;
int n,m,i;
/* Read a number of vertices and process */
while (1)
{
if (scanf("%d",&n) == 1 && n > 0)
{
if (n%2 != 0)
{
continue;
}
57
sg1.nv = n;
sg1.nde = 3*n;
for (i = 0; i < n; ++i)
{
sg1.v[i] = 3*i;
sg1.d[i] = 3;
}
for (i = 0; i < n; i += 2)
{
sg1.e[sg1.v[i]] = i+1;
sg1.e[sg1.v[i+1]] = i;
}
/* Spokes */

sg1.e[sg1.v[i]+1] = i+2;
sg1.e[sg1.v[n-2]+1] = 1;
sg1.e[sg1.v[n-1]+1] = 0;
sg1.e[sg1.v[i]+2] = i-2;
sg1.e[sg1.v[1]+2] = n-2;
sg1.e[sg1.v[0]+2] = n-1;
sg2.nv = n;
sg2.nde = 3*n;
for (i = 0; i < n; ++i)
{
sg2.v[i] = 3*i;
sg2.d[i] = 3;
}
for (i = 0; i < n; ++i)
{
sg2.v[i] = 3*i;
sg2.d[i] = 3;
sg2.e[sg2.v[i]] = (i+1) % n;
58
/* Clockwise */
sg2.e[sg2.v[i]+1] = (i+n-1) % n;
sg2.e[sg2.v[i]+2] = (i+n/2) % n;
/* Diagonals */
}
/* Label sg1, result in cg1 and labelling in lab1; similarly sg2.
It is not necessary to pre-allocate space in cg1 and cg2, but
they have to be initialised as we did above. */
Traces(&sg1,lab1,ptn,orbits,&options,&stats,&cg1);
{
if (n <= 1000)
{
printf("\n");
}
}
else
}
else
break;
}
exit(0);
}
59
14
Variations
As mentioned, nauty and Traces can handle graphs with coloured vertices. In this
section, we describe how several other types of isomorphism problem can be solved by
mapping them onto a problem for vertex-coloured graphs. (But recall that Traces cant
handle directed edges.)
Isomorphism of edge-coloured graphs. Isomorphism of two graphs, each with both
vertices and edges coloured, is defined in the obvious way. An example of such a graph
appears at the left of Figure 3.
1
3
0
2
2
1
0
0
0
0
3
0
1
0
0
2
0
Figure 3: Graphs with coloured edges

In the center of the figure we identify the colours with the integers 1, 2, 3. At the
right of the figure we show an equivalent vertex-coloured graph. In this case there are
two layers, each with its own colour. Edges of colour 1 are represented as an edge in
the first (lowest) layer, edges of colour 2 are represented as an edge in the second layer,
and edges of colour 3 are represented as edges in both layers. It is now easy to see that
the automorphism group of the new graph (precisely, its action on the first layer) is the
automorphism group of the original graph. Moreover, the order in which a canonical
labelling of the new graph labels the vertices of the first layer can be taken to be a
canonical labelling of the original graph.
More generally, if the edge colours are integers in {1, 2, . . . , 2d 1}, we make d layers,
and the binary expansion of each colour number tells us which layers contain edges. The
vertical threads (each corresponding to one vertex of the original graph) can be connected
using either paths or cliques. If the original graph has n vertices
and k colours, the new
graph has O(n log k) vertices. This can be improved to O(n log k) vertices by also using
edges that are not horizontal, but this needs care.
Exchangeable vertex colours. The vertex colours known to nauty and Traces are
distinguishable: vertices can only be mapped onto vertices of the same colour. In some
applications, entire colour classes can also be exchanged.
In the left side of Figure 4 is a graph with three exchangeable vertex colours. To
process this problem with nauty or Traces, we recolour the vertices to be all the same,
then indicate the original colour classes with additional vertices of a new colour, as in the
graph on the right. It is easy to see how this idea can be extended to allow some colours
to be exchangeable and some not.
60
Figure 4: Graphs with exchangeable vertex colours.

Isomorphism of hypergraphs and designs. A hypergraph is similar to an undirected
graph except that the edges can be vertex sets of any size, not just of size 2. Such an
structure is also called a design.
5
1
1
1 1 0 0 0
0 1 1 0 0
0 0 1 1 1
2
3
4
Figure 5: Hypergraph/design isomorphism as graph isomorphism

In the left of Figure 5 we see a hypergraph with 5 vertices, two edges of size 2, and
one edge of size 3. On the right is an equivalent vertex-coloured graph. The vertices on
the left, coloured with one colour, represent the hypergraph edges, while the edges on the
right, coloured with a different colour, represent the hypergraph vertices. The edges of
the graph indicate the hypergraph incidence (containment) relationship.
In the center of the figure, we show the edge-vertex incidence matrix. This can be
any binary matrix at all, which prompts us to note that the problem under consideration
is just that of determining 0-1 matrix equivalence under independent permutation of the
rows and columns. By combining this idea with the previous construction, we can handle
such an equivalence relation on the set of matrices with arbitrary entries.
Hadamard equivalence. Two matrices over {1, +1} are Hadamard-equivalent if one
can be obtained from the other by permuting the rows, permuting the columns, and
multiplying some of the rows and some of the columns by 1.
Suppose A = (aij ) is a matrix over {1, +1} of order m n. Construct a graph G(A)
0
with vertices v1 , . . . , vm , v10 , . . . , vm
of one colour, and w1 , . . . , wn , w10 , . . . , wn0 of another
colour. Insert the edges are {vi , wj } and {vi0 , wj0 } if aij = 1 and {vi , wj0 } and {vi0 , wj } if
aij = 1. Figure 6 gives an example.
61
1 1
1 1
1 1
w1
w2
w3
w10
w20
w30
v1
v2
v3
v10
v20
v30
1
1
1
Figure 6: Hadamard equivalence as graph isomorphism

0
Permuting the rows of A corresponds to permuting v1 , . . . , vm and v10 , . . . , vm
together,
and similarly for permuting the columns. Multiplying row i by 1 corresponds to interchanging vi with vi0 , and similarly with columns. Thus, the operations that define
Hadamard equivalence map onto graph isomorphism operations. It is less obvious that
the same holds in reverse: if B is a second matrix, G(A) is isomorphic to G(B) if and
only if A is Hadamard-equivalent to B [3]. Similarly, Aut(G(A)) consists of the operations corresponding the Hadarmard equivalences of A to itself, together with the central
0
)(w1 w10 ) (wn wn0 ) and a canonical labelling of G(A) can be
element (v1 v10 ) (vm vm
used to make one of A. We omit the details.
Isotopy of matrices. Two matrices over some symbol set S are called isotopic if one
can be obtained from the other by permuting the rows, permuting the columns, and
permuting the symbols. This equivalence relation is important in the study of Latin
squares, quasigroups, and other subjects.
c1
c2
c3
r1
r2
1 3 2
2 1 3
3 2 1
r3
s3
s2
s1
Figure 7: Isotopy as graph isomorphism

Figure 7 shows how to translate isotopy into isomorphism. There are four types of
vertex, with four corresponding colours: one vertex for each row, one vertex for each
column, one vertex for each symbol, and one vertex for each matrix position. The edges
indicate in an obvious fashion what the row, column, and symbol is for each matrix
62
entry. Other related equivalences, such as paratopy (main class isotopy) can be handled
in similar fashion [5].
15
Utilities
The nauty package includes a suite of programs called gtools that provide efficient
processing of files of graphs stored in graph6 or sparse6 format. These formats are
defined in Section 19.
Most of the gtools programs will run on any system with a modern C compiler, but
a few need Unix-like facilities. For example, the program shortg requires a program
compatible with the Unix sort program, as well as pipes.
A general principle is that data is sent to stdout (unless an alternative output file is
named) and diagnostic output is sent to stderr.
All the gtools programs are self-documenting: just execute with the option --help
to see an explanation of all the features. We only list the basic functions of the programs
here; see Section 23 for more details.
geng : generate small graphs
genbg : generate small bicoloured graphs
gentourng : generate small tournaments
gentreeg : generate trees
directg : generate small digraphs with given underlying graph
watercluster2 : a faster alternative to directg written by Gunnar Brinkmann
multig : generate small multigraphs with given underlying graph
vcolg : colour the vertices of graphs in all distinct ways
genrang : generate random graphs
genquartic : generate quartic graphs
genspecialg : generate special graphs, like cycles and complete graphs
copyg : convert format and select subset
labelg : canonically label graphs
shortg : remove isomorphs from a file of graphs
listg : display graphs in a variety of forms
showg : a stand-alone subset of listg
amtog : read graphs in adjacency matrix form
dretog : read graphs in dreadnaut form
complg : complement graphs
converseg : converse digraphs
63
catg : concatenate files of graphs

addedgeg : add an edge in each possible way
deledgeg : delete an edge in each possible way
newedgeg : in each possible way, subdivide two non-adjacent edges and join the two new
vertices
NRswitch : switch the edges between the neighbourhood and the complementary neighbourhood, for each vertex
countg : count graphs according to a variety of properties
pickg : select graphs according to a variety of properties
biplabg : label bipartite graphs so the colour classes are contiguous
linegraphg : make the linegraphs of a file of graphs
subdivideg : make the subdivision graphs of a file of graphs
ranlabg : randomly relabel graphs
planarg : test graphs for planarity and find embeddings or obstructions. The planarity
code uses the method of Boyer and Myrvold [1] and was programmed by Paulette
Lieby for the Magma project.
cubhamg : find hamiltonian cycles in subcubic graphs
hamheuristic : try to find hamiltonian cycles in any graphs
twohamg : split quartic graphs into two hamiltonian cycles
Further programs will be added. Requests are welcome.
16
Installing nauty and Traces
nauty is prepared using the autoconf configuration system. You need a C compiler and
library at least recent enough to support the basic commands of ANSI C.
If you have a Unix-like operating system, which includes Linux, MacOSX or a Windows environment such as cygwin, first run the configuration script like this:
./configure
That will examine the facilities available on your computer and generate a custom makefile
and custom definition files nauty.h, gtools.h and naututil.h. Then run
make
to compile the basic files of nauty and Traces.
This will generate the executable file dreadnaut and a lot of object files and libraries.
For compiling your own programs, the most convenient way to link with nauty or Traces
is to use the static library nauty.a. For example, with the gcc compiler, a simple compilation might be
gcc -o myprog myprog.c nauty.a
64
Execution of make without arguments will also generate the library nauty1.a, which is
the same except that MAXN is defined to be equal to WORDSIZE. This is more efficient
if you only want to process small graphs.
For both nauty.a and nauty1.a, WORDSIZE is determined automatically as specified
in Section 3. However, there may be times when you want to use a particular word size,
so you can also make the following variants by, for example, make nautyL1.a :
nautyW.a: WORDSIZE = 32, unlimited MAXN
nautyW1.a: WORDSIZE = MAXN = 32
nautyL.a: WORDSIZE = 64, unlimited MAXN
nautyL1.a: WORDSIZE = MAXN=64
The last two variants can only be used if your compiler supports either unsigned
long or unsigned long long type as a 64-bit integer.
To use these versions, you need to compile your program in the same way. For example:
gcc -o myprog -DWORDSIZE=64 -DMAXN=WORDSIZE myprog.c nautyL1.a
Using the function nauty check( ) in your program is a way to check that you compiled it correctly; see Section 11.
There are some test files included in the package. To run these, just use
make checks
followed by
./runalltests
which should not produce any output that looks like an error message.
If you are on a system where configure doesnt work or make is not available,
you should start by editing the definitions near the start of nauty.h, naututil.h and
gtools.h. (Most should be OK already.) Then you can compile using the commands in
makefile.basic as a guide.
Some compilation options are provided at the configure stage. Run
./configure --help to see the syntax and more information.
(a) The choice of compiler, compiler options, linker options, libraries and include files
can be influenced by the environment variables CC, CFLAGS, LDFLAGS, LIBS and
CPPFLAGS. For example, to compile a 32-bit program on a 64-bit Intel system, this
might work (assuming a Bourne-type shell such as bash):
CFLAGS=-m32 LDFLAGS=-m32 ./configure
(Note that the hardware 32/64-bit mode is entirely independent of the value of
WORDSIZE.)
(b) Section 3 describes how WORDSIZE is chosen when no explicit definition of it appears. To override this default rule, you can use
./configure --enable-wordsize=NN
where NN is 16, 32 or 64. However, an explicit definition of WORDSIZE at compile
time takes precedence even over this.
65
(c) Generally nauty and Traces are not thread-safe. However, if your compiler supports
thread-local storage, configuring with
./configure --enable-tls
will mark static and external variables as thread-local. (The most common syntax is
to add the attribute thread.) This means that nauty or Traces can be invoked
at the same time by different threads. This may slow it down slightly if you arent
using threads. There are sample programs nauthread1.c and nauthread2.c in the
distribution.
(d) Some C compilers and processors support commands like builtin clz( ) that locate the first 1-bit in a word faster than nautys standard macros can do it. These are
detected automatically and influence the definition of the FIRSTBIT and TAKEBIT
macros. However, if this causes trouble for some reason, you can turn off this feature
using
./configure --disable-clz
(e) Many modern processors have an instruction POPCNT that counts 1-bits. It will
be used to define the macro POPCOUNT if possible. To disable this feauture, use
./configure --disable-popcnt
(f) The output written by Traces and some of the output written by dreadnaut will
look prettier on terminals that support ANSI control sequences if you use
./configure --enable-ansicontrols
Dont use this if you plan to read dreadnaut output with a program.
(g) If your operating system allows it, dreadnaut establishes a signal handler for catching
SIGINT when nauty or Traces is running. To disable this feature, use
./configure --disable-interrupt
This only effects dreadnaut.
17
Recent changes
See the file changes24-26.txt for a list of changes made since version 2.4.
18
More on automorphism groups
nauty and Traces use the Random Schreier Method to process the automorphism group
as it is found. For nauty, this is optional: see the field schreier of the options. Difficult
graphs with substantial automorphism groups will benefit the most from this addition.
The Random Schreier Method is a probabilistic algorithm that determines information
about the group only with some probability. However, this nondeterminism does not effect
the result of nauty or Traces. Occasionally a different set of generators will be found,
but the group generated will be the same and the canonical labelling will be unaffected.
There is a parameter for tuning the method, which can be changed using the function
schreier fails( ). See the file schreier.txt for documentation of this and the other
66
group functions. The default value is 10, but smaller values may be better if the group is
very large. In dreadnaut, the G command sets this parameter.
18.1
Listing the full automorphism group
The automorphism group of a graph can be exceedingly large, so trying to list it all
might be a bad idea. However, it can be done using the code in the files naugroup.h and
naugroup.c, as illustrated by the following program.
This works with sparse nauty as well, but not with Traces.
67
18.2
nautyex3.c : Listing the whole automorphism group
/* This program prints the entire automorphism group of an n-vertex

polygon, where n is a number supplied by the user.
*/
#include "nauty.h"
/* which includes <stdio.h> */
#include "naugroup.h"
/**************************************************************************/
void
writeautom(int *p, int n)
/* Called by allgroup. Just writes the permutation p. */
{
int i;
for (i = 0; i < n; ++i) printf(" %2d",p[i]); printf("\n");
}
/**************************************************************************/
int
{
DYNALLSTAT(graph,g,g_sz);
statsblk stats;
int n,m,v;
grouprec *group;
/* The following cause nauty to call two procedures which
store the group information as nauty runs. */
options.userautomproc = groupautomproc;
options.userlevelproc = grouplevelproc;
while (1)
{
if (scanf("%d",&n) == 1 && n > 0)
{
68
DYNALLOC2(graph,g,g_sz,m,n,"malloc");
EMPTYGRAPH(g,m,n);
for (v = 0; v < n; ++v) ADDONEEDGE(g,v,(v+1)%n,m);
printf("Automorphisms of C[%d]:\n",n);
/* Get a pointer to the structure in which the group information
has been stored. If you use TRUE as an argument, the
structure will be "cut loose" so that it wont be used
again the next time nauty() is called. Otherwise, as
here, the same structure is used repeatedly. */
group = groupptr(FALSE);
/* Expand the group structure to include a full set of coset
representatives at every level. This step is necessary
if allgroup() is to be called. */
makecosetreps(group);
/* Call the procedure writeautom() for every element of the group.
The first call is always for the identity. */
allgroup(group,writeautom);
}
else
break;
}
exit(0);
}
18.3
Giving known generators to Traces
Traces provides the possibility of giving it known automorphisms. This is only likely to
be useful for very regular graphs that have automorphisms which are difficult to discover.
The method is illustrated in the following sample program.
69
18.4
nautyex9.c : Giving known generators to Traces
/* This program demonstrates how known automorphisms can be given

to Traces. We compute the automorphism group of the circulant
graph of order n with i is adjacent to j iff j-i is a square
mod n. We need that -1 is a square so that the graph is
undirected, which means that the prime factors of n must be
congruent to 1 mod 4. (This is the Paley graph in the event
that p is a prime.)
*/
#include "traces.h"
int
{
DYNALLSTAT(int,p,p_sz);
DYNALLSTAT(boolean,issquare,issquare_sz);
TracesStats stats;
SG_DECL(sg);
int deg,n,m,i,j;
size_t k;
permnode *gens;
/* Select option for passing generators to Traces */
options.generators = &gens;
/* Read a number of vertices and process it */
while (1)
{
if (scanf("%d",&n) == 1 && n > 2)
{
70
DYNALLOC1(int,p,p_sz,n,"malloc");
DYNALLOC1(boolean,issquare,issquare_sz,n,"malloc");
/* Initialise list of automorphisms */
gens = NULL;
/* Find the squares and the degree */
for (i = 0; i < n; ++i) issquare[i] = FALSE;
for (i = 0; i < n; ++i) issquare[(i*i)%n] = TRUE;
if (!issquare[n-1])
{
printf("-1 must be a square mod n; try again\n");
continue;
}
deg = 0;
for (i = 1; i < n; ++i) if (issquare[i]) ++deg;
/* Now make the graph */
SG_ALLOC(sg,n,n*deg,"malloc");
sg.nv = n;
sg.nde = n*deg;
for (i = 0; i < n; ++i)
{
sg.v[i] = i*deg;
sg.d[i] = deg;
}

for (i = 0; i < n; ++i)

/* Edges */
{
k = sg.v[i];
for (j = 1; j < n; ++j)
if (issquare[j]) sg.e[k++] = (i + j) % n;
}
/* Add known automorphisms */
/* We wouldnt need freeschreier() if we were only
processing one graph, but it doesnt hurt. This
is how to properly dispose of previous generators. */
freeschreier(NULL,&gens);
/* Cyclic rotation */
71
for (i = 0; i < n; ++i) p[i] = (i + 1) % n;

addpermutation(&gens,p,n);
/* Reflection about 0 */
for (i = 0; i < n; ++i) p[i] = (n - i) % n;
addpermutation(&gens,p,n);
/* Call Traces */
Traces(&sg,lab,ptn,orbits,&options,&stats,NULL);
printf("\n");
/* Traces left the automorphims we gave it, augmented by
any extra automorphims it found, in a circular list
pointed to by gens. See schreier.txt for documentation. */
}
else
break;
}
exit(0);
}
72
18.5
nautyex10.c : Two-step canonical labelling with Traces
Traces uses a different tree-traversal method when it only wants to compute the automorphism group only, without canonical labelling. For some types of difficult graphs, this
can be much faster than canonical labelling.
Since Traces can also make use of known automorphisms, it is sometimes faster to
compute the group first and then use the group for computing the canonical labelling. In
dreadnaut this is achieved with the sequence P -c x c x. The following illustrates how
to achieve the same in a program.
An extension (not shown) would be to use the orbit sizes from the first computation
to partition the graph before the second computation.

This version uses Traces and demonstrates how to compute the
automorphism group separately before computing the canonical
labelling. Although this is slower for easy graphs like
those here, it can be faster for some very difficult graphs.
*/
#include "traces.h"
int
{
TracesStats stats;
permnode *generators;
int n,m,i;
/* Read a number of vertices and process */
while (1)
{
if (scanf("%d",&n) == 1 && n > 0)
{
73
if (n%2 != 0)
{
continue;
}
sg1.nv = n;
sg1.nde = 3*n;
for (i = 0; i < n; ++i)
{
sg1.v[i] = 3*i;
sg1.d[i] = 3;
}
for (i = 0; i < n; i += 2)
{
sg1.e[sg1.v[i]] = i+1;
sg1.e[sg1.v[i+1]] = i;
}
/* Spokes */

sg1.e[sg1.v[i]+1] = i+2;
sg1.e[sg1.v[n-2]+1] = 1;
sg1.e[sg1.v[n-1]+1] = 0;
sg1.e[sg1.v[i]+2] = i-2;
sg1.e[sg1.v[1]+2] = n-2;
sg1.e[sg1.v[0]+2] = n-1;
sg2.nv = n;
sg2.nde = 3*n;
74
for (i = 0; i < n; ++i)

{
sg2.v[i] = 3*i;
sg2.d[i] = 3;
}
for (i = 0; i < n; ++i)
{
sg2.v[i] = 3*i;
sg2.d[i] = 3;
sg2.e[sg2.v[i]] = (i+1) % n;
sg2.e[sg2.v[i]+1] = (i+n-1) % n;
sg2.e[sg2.v[i]+2] = (i+n/2) % n;
}
/* Clockwise */
/* Diagonals */
/* Now we make the canonically labelled graphs by a two-step

process. The first call to Traces computes the
automorphism group. The second call computes the
canonical labelling, using the automorphism group from
the first call.
We have declared a variable "generators" that will be
used to hold the group generators between the two calls.
It has to be initialised to NULL and its address has to
be given to Traces using options.generators. After the
second call, we need to discard the generators with a
call to freeschreier(), which also initializes it again. */
generators = NULL;
options.generators = &generators;
options.getcanon = FALSE;
Traces(&sg1,lab1,ptn,orbits,&options,&stats,NULL);
freeschreier(NULL,&generators);
options.getcanon = FALSE;
Traces(&sg2,lab1,ptn,orbits,&options,&stats,NULL);
freeschreier(NULL,&generators);
{
75
if (n <= 1000)
{
printf("\n");
}
}
else
}
else
break;
}
exit(0);
}
76
19
Graph formats used by the utilities
This is the file formats.txt.
Description of graph6, sparse6 and digraph6 encodings

----------------------------------------------------Brendan McKay, [email protected]
Updated Jun 2015.
General principles:
All numbers in this description are in decimal unless obviously
in binary.
Apart from the header, there is one object per line. Apart from
the header, end-of-line characters, and the characters ":", ";"
and "&" which might start a line, all bytes have a value in the
range 63-126 (which are all printable ASCII characters). A file of
objects is a text file, so whatever end-of-line convention is
locally used is fine; however the C library input routines must
show the standard single-LF end of line to programs).
Bit vectors:
A bit vector x of length k can be represented as follows.
Example: 1000101100011100
(1) Pad on the right with 0 to make the length a multiple of 6.
Example: 100010110001110000
(2) Split into groups of 6 bits each.
Example: 100010 110001 110000
(3) Add 63 to each group, considering them as bigendian binary numbers.
Example: 97 112 111
These values are then stored one per byte.
So, the number of bytes is ceiling(k/6).
Let R(x) denote this representation of x as a string of bytes.
Small nonnegative integers:
Let n be an integer in the range 0-68719476735 (2^36-1).
If 0 <= n <= 62, define N(n) to be the single byte n+63.
77
If 63 <= n <= 258047, define N(n) to be the four bytes

126 R(x), where x is the bigendian 18-bit binary form of n.
If 258048 <= n <= 68719476735, define N(n) to be the eight bytes
126 126 R(x), where x is the bigendian 36-bit binary form of n.
Examples:
N(30) = 93
N(12345) = N(000011 000000 111001) = 126 66 63 120
N(460175067) = N(000000 011011 011011 011011 011011 011011)
= 126 126 63 90 90 90 90 90
Description of graph6 format.

---------------------------Data type:
simple undirected graphs of order 0 to 68719476735.
Optional Header:
>>graph6<<
(without end of line!)
File name extension:

.g6
One graph:
Suppose G has n vertices. Write the upper triangle of the adjacency
matrix of G as a bit vector x of length n(n-1)/2, using the ordering
(0,1),(0,2),(1,2),(0,3),(1,3),(2,3),...,(n-1,n).
Then the graph is represented as
N(n) R(x).
Example:
Suppose n=5 and G has edges 0-2, 0-4, 1-3 and 3-4.
x = 0 10 010 1001
Then N(n) = 68 and R(x) = R(010010 100100) = 81 99.
So, the graph is 68 81 99.
Description of sparse6 format.

-----------------------------Data type:
Undirected graphs of order 0 to 68719476735.
Loops and multiple edges are permitted.
Optional Header:
>>sparse6<<
78

.s6
General structure:
Each graph occupies one text line. Except for the first character
and end-of-line characters, each byte has the form 63+x, where
0 <= x <= 63. The byte encodes the six bits of x.
The encoded graph consists of:
(1) The character :.
(This is present to distinguish
the code from graph6 format.)
(2) The number of vertices.
(3) A list of edges.
(4) end-of-line
Loops and multiple edges are supported, but not directed edges.
Number of vertices n:
1, 4, or 8 bytes N(n) as above.
This is the same as graph6 format.
List of edges:
Let k be the number of bits needed to represent n-1 in binary.
The remaining bytes encode a sequence
b[0] x[0] b[1] x[1] b[2] x[2] ... b[m] x[m]
Each b[i] occupies 1 bit, and each x[i] occupies k bits.
Pack them together in bigendian order, and pad up to a
multiple of 6 as follows:
1. If (n,k) = (2,1), (4,2), (8,3) or (16,4), and vertex
n-2 has an edge but n-1 doesnt have an edge, and
there are k+1 or more bits to pad, then pad with one
0-bit and enough 1-bits to complete the multiple of 6.
2. Otherwise, pad with enough 1-bits to complete the
multiple of 6.
These rules are to match the gtools procedures, and to avoid
the padding from looking like an extra loop in unusual cases.
Then represent this bit-stream 6 bits per byte as indicated above.
The vertices of the graph are 0..n-1.
The edges encoded by this sequence are determined thus:
79
v = 0
for i from 0 to m do
if b[i] = 1 then v = v+1 endif;
if x[i] > v then v = x[i] else output {x[i],v} endif
endfor
In decoding, an incomplete (b,x) pair at the end is discarded.
Example:
:Fa@x^
: indicates sparse6 format.
Subtract 63 from the other bytes and write them in binary,
six bits each.
000111 100010 000001 111001 011111
The first byte is not 63, so it is n. n=7
n-1 needs 3 bits (k=3). Write the other bits in groups
of 1 and k:
1 000
1 000
0 001
1 110
0 101
1 111
This is the b/x sequence 1,0 1,0 0,1 1,6 0,5 1,7.
The 1,7 at the end is just padding.
The remaining parts give the edges 0-1 0-2 1-2 5-6.
Description of incremental sparse6 format.

----------------------------------------This is an extension to sparse6 format that is very efficient if most
graphs in a file are similar to the previous graph.
Each graph occupies one text line. Except for the first character
and end-of-line characters, each byte has the form 63+x, where
0 <= x <= 63. The byte encodes the six bits of x.
The encoded graph consists of:
(1) The character ;.
(2) A list of edges.
(3) end-of-line
This cannot appear as the first graph in a file. The number of vertices
is taken to be equal to the number of vertices in the previous graph.
The list of edges specifies the symmetric difference of this graph and
80
the previous graph.

sparse6 format.
It is encoded exactly the same as part (3) of
Loops are supported, but not multiple edges.
Description of digraph6 format.

-----------------------------Data type:
simple directed graphs (allowing loops) of order 0 to 68719476735.
Optional Header:
>>digraph6<<

.d6
One graph:
Suppose G has n vertices. Write the adjacency matrix of G
as a bit vector x of length n^2, row by row.
Then the graph is represented as & N(n) R(x).
The character & (decimal 38) appears as the first character.
Example:
Suppose n=5 and G has edges 0->2, 0->4, 3->1 and 3->4.
x = 00101 00000 00000 01001 00000
Then N(n) = 68 and
R(x) = R(00101 00000 00000 01001 00000) = 73
So, the graph is 38 68 73 63 65 79 63.
63
65
79
63.
For a description of the planarcode and edgecode formats, see the plantri documentation at http://cs.anu.edu.au/bdm/plantri.
20
Other ways to use nauty
If you want to use nauty in a richer interactive environment, some of your choices are:
(a) Magma: http://magma.maths.usyd.edu.au/magma
(b) GAP with GRAPE: http://www.maths.qmul.ac.uk/leonard/grape/
(c) LINK: http://dimacs.rutgers.edu/berryj/LINK.html
(d) Sage-combinat: http://mupad-combinat.sourceforge.net/
(e) Macaulay2: http://mupad-combinat.sourceforge.net/
81
21
Licence details
For the copyright status of items in the package, see the file COPYRIGHT. They are free
for use with very limited restrictions.
If you use nauty or Traces in your published research, please cite our paper [10].
22
Acknowledgements
So many people have made contributions to nauty that listing them all would be futile.
Bill Kocay, Kevin Malysiak, Andrew Kirk and Gordon Royle stand out, but many people
have made large and small contributions. Some code is derived from other peoples programs: thanks to Frank Ruskey in regard to gentreeg and to Narjess Afzaly in regard to
genquarticg. Heart-felt thanks to all of you.
The authors would appreciate receiving any comments about the program and/or this
Guide, especially about apparent bugs.
82
23
Help texts for the utilities
===== addedgeg ======================================================

Usage: addedgeg [-lq] [-D#] [-btfF] [-z#] [infile [outfile]]
For each edge nonedge e, output G+e if it satisfies certain conditions
The output file has a header if and only if the input file does.
-l
-D#
-b
-t
-f
-F
-z#
-q
Canonically label outputs

Specify an upper bound on the maximum degree of the output
Output has no new cycles of odd length
Output has no new 3-cycle if input doesnt
Output has no new cycles of length less than #
-btfFz can be used in arbitrary combinations
Suppress auxiliary information
===== amtog ======================================================

Usage: amtog [-n#sgzhq] [-o#] [infile [outfile]]
Read graphs in matrix format.
-n#
-g
-s
-z
-h
-w
-q
-o#
Set the initial graph order to # (no default).

This can be overridden in the input.
Write the output in graph6 format (default).
Write the output in sparse6 format.
Write the output in digraph6 format.
Write a header (according to -g or -s).
Dont warn about loops (which are suppressed for -g)
Suppress auxiliary information.
Treat digit # as 1 and other digits as 0.
Input consists of a sequence of commands restricted to:

n=#
m
M
t
T
q
set number of vertices (no default)

The = is optional.
Matrix to follow
An m is also assumed if a digit is encountered.
Complement of matrix to follow (as m)
Upper triangle of matrix to follow, row by row
excluding the diagonal.
Complement of upper trangle to follow (as t)
exit (optional)
83
===== biplabg ======================================================

Usage: biplabg [-q] [infile [outfile]]
Label bipartite graphs so that the colour classes are contiguous.
The first vertex of each component is assigned the first colour.
Vertices in each colour class have the same relative order as before.
Non-bipartite graphs are rejected.
-q
===== catg ======================================================

Usage: catg [-xv] [infile]...
Copy files to stdout with all but the first header removed.
-x
Dont write a header.

In the absence of -x, a header is written if
there is one in the first input file.
-v
Summarize to stderr.
===== complg ======================================================

Usage: complg [-lq] [-r|-R] [infile [outfile]]
Take the complements of a file of graphs.
The output format is defined by the header or first graph.
-r
-R
-L
-l
-q
Only complement if the complement has fewer directed edges.

Only complement if the complement has fewer directed edges
or has the same number of directed edges and is canonically
less than the original.
Complement the loops too. By default, preserve them.
Canonically label outputs.
===== converseg ======================================================

Usage: converseg [-q] [infile [outfile]]
Take the converse digraphs of a file of graphs.
84
Undirected graphs are passed through without change, while
directed graphs are written in digraph6 format.
-q
===== copyg ======================================================

Usage: copyg [-gszfp#:#qhx] [infile [outfile]]
Copy a file of graphs with possible format conversion.
-g Use graph6 format for output
-s Use sparse6 format for output
-z Use digraph6 format for output
-i Use incremental sparse6 format for output
In the absence of -g, -s, -z or -i, the format
depends on the header or, if none, the first input line.
As an exception, digraphs are always written in digraph6.
-p# -p#:#
Specify range of input lines (first is 1)
This can fail if the input has incremental lines.
-f With -p, assume input lines of fixed length
(ignored if header or first line has sparse6 format).
-I# Have at most this number of incremental steps
in a row. Implies -i.
-h Write a header.
-x Dont write a header.
In the absence of -h and -x, a header is written if
there is one in the input.
-q
Suppress auxiliary output.
===== countg ======================================================

Usage: [pickg|countg] [-fp#:#q -V] [--keys] [-constraints -v] [ifile [ofile]]
countg : Count graphs according to their properties.
pickg : Select graphs according to their properties.
ifile, ofile : Input and output files.
- and missing names imply stdin and stdout.
Miscellaneous switches:
-p# -p#:#
85
May fail if input is incremental.

-f
With -p, assume input lines of fixed length
(only used with a file in graph6/digraph6 format)
-v
Negate all constraints
-V
List properties of every input matching constraints.
-l
Put a blank line whenever the first parameter changes,
if there are at least two parameters.
-q
Suppress informative output.
Constraints:
Numerical constraints (shown here with following #) can take
a single integer value, or a range like #:#, #:, or :#. Each
can also be preceded by ~, which negates it.
(For example,
-~D2:4 will match any maximum degree which is _not_ 2, 3, or 4.)
Constraints are applied to all input graphs, and only those
which match all constraints are counted or selected.
-n#
-L#
-d#
-m#
-u#
-s#
-r
-z#
-g#
-T#
-B#
-H#
-E
-a#
-c#
-i#
-j#
number of vertices
-e# number of edges
number of loops
-C
strongly connected
minimum (out-)degree
-D# maximum (out-)degree
vertices of min (out-)degree -M# vertices of max (out-)degree
minimum (in-)degree
-U# maximum (in-)degree
vertices of min (out-)degree -S# vertices of max (out-)degree
regular
-b
bipartite
radius
-Z# diameter
girth (0=acyclic)
-Y# total number of cycles
number of triangles
-K# number of maximal cliques
smallest side of some bipartition (0 if none)
number of induced cycles
Eulerian (all degrees are even, connectivity not required)
group size -o# orbits -F# fixed points -t vertex-transitive
connectivity (only implemented for 0,1,2).
min common nbrs of adjacent vertices;
-I# maximum
min common nbrs of non-adjacent vertices; -J# maximum
Sort keys:
Counts are made for all graphs passing the constraints. Counts
are given separately for each combination of values occurring for
the properties listed as sort keys. A sort key is introduced by
-- and uses one of the letters known as constraints. These can
be combined: --n --e --r is the same as --ne --r and --ner.
The order of sort keys is significant.
The output format matches the input, except that sparse6 is used
to output an incremental graph whose predecessor is not output.
===== cubhamg ======================================================
>E Usage: cubhamg [-#] [-v | -V] [-n#-#] [-y#-#] [infile [outfile]]
86
===== deledgeg ======================================================

Usage: deledgeg [-lq] [-d#] [-z] [infile [outfile]]
For each edge e, output G-e
-z
-l
-d#
-q
Consider as digraph and delete directed edges

Specify a lower bound on the minimum out-degree of the output
===== delptg ======================================================

Usage: delptg [-lq] [-d#|d#:#] [-n#] [infile [outfile]]
Delete some vertices from a file of graphs.
No isomorph reduction is done.
-l Canonically label outputs
-d# -d#:# Only remove vertices with original degree in the given range
For digraphs, the out-degree is used.
-n# The number of vertices to delete (default 1).
Inputs that are too small are ignored; no empty graphs are output.
-q Suppress auxiliary information
===== directg ======================================================
Usage: directg [-q] [-u|-T|-G] [-V] [-o] [-f#] [-e#|-e#:#] [-s#/#] [infile [outfile]]
Read undirected graphs and orient their edges in all possible ways.
Edges can be oriented in either or both directions (3 possibilities).
Isomorphic directed graphs derived from the same input are suppressed.
If the input graphs are non-isomorphic then the output graphs are also.
-e# | -e#:# specify a value or range of the total number of arcs
-o
orient each edge in only one direction, never both
-f# Use only the subgroup that fixes the first # vertices setwise
-T
-G
-V
-u
use a simple text output format (nv ne edges) instead of digraph6

like -T but includes group size as third item (if less than 10^10)
The group size does not include exchange of isolated vertices.
only output graphs with nontrivial groups (including exchange of
isolated vertices). The -f option is respected.
no output, just count them
87
-s#/#
-q
Make only a fraction of the orientations: The first integer is

the part number (first is 0) and the second is the number of
parts. Splitting is done per input graph independently.
suppress auxiliary information
===== dretodot ======================================================

Usage: dretodot [-S#:#ixF#o#m#n#r#:#[r#]d#g] [infile.dre [outfile.dot [outfile.dre]]]
Read graphs and initial coloring in dreadnaut format.
Write graphs in dot format to outfile.dot.
If outfile.dre is given, write the input graph and the partition,
as modified by the -F and -i options, to outfile.dre. outfile.dre
is allowed to be the same file as infile.dre.
-V
Set max number of vertices (default 1000).
-E
Set max number of edges (default 5000).
-v
Set verbose mode (default NO).
-S#:# Set maximum width and height of the drawing, in inches
(default 10 x 6.18).
-i
Refine the partition before drawing (default NO).
-x
Draw the orbit partition, computed by Traces. (default NO).
-F#
Individualize vertex # (and refine the partition).
-o#
Label vertices starting at # (default 0). This can be
overridden in the input.
-m#
Set the drawing model (see http://www.graphviz.org):
0 (or any value different from 1,...,5)=dot (default 0),
1=neato, 2=fdp, 3=sfdp, 4=twopi, 5=circo.
-n#
Scale the size of vertices in the drawing (#=0,1,2; default 1).
-r#:# (-r#) Set the vertices to be drawn at the topmost level
in a hierarchical (dot model) drawing (default none).
Any sequence of -r#:# (r#) options is allowed.
-d#
Draw the graph induced by vertices at topmost level
and by vertices at distance # from them; example:
./dretodot -n2 -r1 -r12:17 -d2 MyGraph.dre Outfile.dot.
-g
Highlight the induced subgraph into the whole graph.
===== dretog ======================================================
Usage: dretog [-n#o#sghq] [infile [outfile]]
Read graphs in dreadnaut format.
-o#
-n#
-g
-z
Label vertices starting at # (default 0).

Set the initial graph order to # (no default).
Use graph6 format (default for undirected graphs).
Use digraph6 format (default for directed graphs).
88
-s
-h
-q
Use sparse6 format.

Write a header (according to -g, -z or -s).
Suppress auxiliary output.
Input consists of a sequence of dreadnaut commands restricted to:

n=#
set number of vertices (no default)

The = is optional.
$=#
set label of first vertex (default 0)
The = is optional.
d
indicate graph will be directed
$$
return origin to initial value (see -o#)
".." and !..\n
comments to ignore
g
specify graph to follow (as dreadnaut format)
Can be omitted if first character of graph is a digit or ;.
q
exit (optional)
===== genbg ======================================================
Usage: genbg [-c -ugs -vq -lzF] [-Z#] [-D#] [-A] [-d#|-d#:#] [-D#|-D#:#] n1 n2
[mine[:maxe]] [res/mod] [file]
Find all bicoloured graphs of a specified class.
n1
: the number of vertices in the first class
n2
: the number of vertices in the second class
mine:maxe : a range for the number of edges
#:0 means # or more except in the case 0:0
res/mod : only generate subset res out of subsets 0..mod-1
file : the name of the output file (default stdout)
-c
: only write connected graphs
-z
: all the vertices in the second class must have
different neighbourhoods
-F
: the vertices in the second class must have at least two
neighbours of degree at least 2
-L
: there is no vertex in the first class whose removal leaves
the vertices in the second class unreachable from each other
-Z#
: two vertices in the second class may have at most # common nbrs
-A
: no vertex in the second class has a neighbourhood whith is a
subset of another vertex in the second class
-D#
: specify an upper bound for the maximum degree
Example: -D6. You can also give separate maxima for the
two parts, for example: -D5:6
-d#
: specify a lower bound for the minimum degree.
Again, you can specify it separately for the two parts: -d1:2
-g
: use graph6 format for output (default)
-s
: use sparse6 format for output
-a
: use Greechie diagram format for output
89
-u
-v
-l
: do not output any graphs, just generate and count them

: display counts by number of edges to stderr
: canonically label output graphs (using the 2-part colouring)
-q
: suppress auxiliary output
See program text for much more information.

===== geng ======================================================
Usage: geng [-cCmtfbd#D#] [-uygsnh] [-lvq]
[-x#X#] n [mine[:maxe]] [res/mod] [file]
Generate all graphs of a specified class.
n
: the number of vertices
mine:maxe : a range for the number of edges
#:0 means # or more except in the case 0:0
-c
-C
-t
-f
-b
:
:
:
:
:
-m
-d#
-D#
-v
-l
:
:
:
:
only write connected graphs

only write biconnected graphs
only generate triangle-free graphs
only generate 4-cycle-free graphs
only generate bipartite graphs
(-t, -f and -b can be used in any combination)
save memory at the expense of time (only makes a
difference in the absence of -b, -t, -f and n <= 28).
a lower bound for the minimum degree
a upper bound for the maximum degree
display counts by number of edges
canonically label output graphs
-u
-g
-s
-y
-h
:
:
:
:
:
do not output any graphs, just generate and count them

use graph6 output (default)
use sparse6 output
use the obsolete y-format instead of graph6 format
for graph6 or sparse6 format, write a header too
-q
: suppress auxiliary output (except from -v)

===== genrang ======================================================
Usage: genrang [-P#|-P#/#|-e#|-r#|-R#|-d#] [-l#] [-m#] [-t] [-T] [-a]
[-s|-g|-z] [-S#] [-q] n|n1,n2 num [outfile]
90
Generate random graphs.

n : number of vertices
n1,n2 : number of vertices (bipartite graph)
num : number of graphs
A bipartite variant is only available if specified below.
-s :
-g :
-z :
-P#/#
-e# :
-r# :
-d# :
-R# :
-l#
-m#
-t
-T
-a
-S#
-q
:
:
:
:
:
:
:
Write in sparse6 format (default)

Write in graph6 format
Make random digraphs and write in digraph6 format
: Give edge probability; -P# means -P1/#.
Bipartite version available.
Give the number of edges
Bipartite version available.
Make regular of specified degree
Make regular of specified degree (pseudorandom)
Bipartite version: this is the degree on the first side
Make regular of specified degree but output
as vertex count, edge count, then list of edges
Maximum loop multiplicity (default 0)
Maximum multiplicity of non-loop edge (default and minimum 1)
Make a random tree
Make a random tournament (implies -z)
Make invariant under a random permutation
Specify random generator seed (default nondeterministic)
suppress auxiliary output
===== genquarticg ======================================================

Usage: genquarticg [-ugs -h -c -l] n [res/mod] [file]
generate all non-isomorphic quartic graphs of a given order
n
:
file :
-u
:
-g
:
-s
:
-h
-c
:
-C
:
res/mod
-l
:
the number of the vertices

the name of the output file (default stdout)
use graph6 format for output (default)
use sparse6 format for output
write a header (only with -g or -s).
only write connected graphs
only write biconnected graphs
: only generate subset res out of subsets 0..mod-1
canonically label output graphs.
===== genspecialg ======================================================
Usage: genspecialg
[-s|-g|-z|-d] [-q] [-p#|-c#|-e#|-k#|-b#,#|-Q#|-f#|-J#,#|-P#,#|C#,#...|G#,#...|T#,#...] [outfile
91
Generate one particular graph.

# : size parameter called n in the descriptions
-s
-g
-z
-d
-q
:
:
:
:
:
Write in sparse6 format (default)

Write in graph6 format
Make digraph versions and write in digraph6 format
Write in dreadnaut format (can be used with -z)
Suppress summary
If defined, the digraph version is shown in parentheses:

-p#
: path (directed path) on n vertices.
-c#
: cycle (directed cycle) on n vertices.
-e#
: empty graph (digraph with loops only) on n vertices.
-k#
: complete graph (with loops) on n vertices
-b#,# : complete bipartite graph (directed l->r) on n vertices
-f#
: flower snark on 4*# vertices
-P#,# : generalized Petersen graph; usual one is -P5,2
-Q#
: hypercube on 2^n vertices and degree n.
-J#,# : Johnson graph J(n,k), args are n and k.
-C#,#... : circulant (di)graph.
-T#,#... : theta (di)graph Theta(#,#,...), give path lengths.
-G#,#... : (directed) grid, use negative values for open directions
===== gentourng ======================================================
Usage: gentourng [-cd#D#] [-ugsz] [-lq] n [res/mod] [file]
Generate all tournaments of a specified class.
n
-c
-d#
-D#
-l
:
:
:
:
only write strongly-connected tournaments

a lower bound for the minimum out-degree
a upper bound for the maximum out-degree
canonically label output graphs
-u
: do not output any graphs, just generate and count them
-g
: use graph6 output (lower triangle)
-s
: use sparse6 output (lower triangle)
-z
: use digraph6 output
-h
: write a header (only with -g or -s)
Default output is upper triangle row-by-row in ascii
-q
92
===== gentreeg ======================================================

Usage: gentreeg [-D#] [-Z#:#] [-ulps] [-q] n [res/mod] [file]
Generate (unrooted) trees.
n
-D#
: a upper bound for the maximum degree
-Z#:# : bounds for the diameter
-s
-p
-l
-u
:
:
:
:
use sparse6 output (default)

write a parent array
write a level array
-q

===== hamheuristic ======================================================
Usage: hamheuristic [-sgu] [-vq] [-L#] [-t#] [infile [outfile]]
Apply a heuristic for finding hamiltonian cycles.
Output those which are unsuccessful.
-s
-g
-u
force output to sparse6 format

force output to graph6 format
If neither -s or -g are given, the output format is
determined by the header or, if there is none, by the
format of the first input graph.
Suppress output to outfile, give statistics instead.
The output file will have a header if and only if the input file does.
-p
-v
-L#
-t#
Be content with a hamiltonian path

Give a cycle or path if one is found.
Limit number of sideways steps (default 1000+5*n)
Try # times (default 1)
-q
===== labelg ======================================================

Usage: labelg [-q] [sg | C#W#] [-fxxx] [-S|-t] [-i# -I#:# -K#] [infile [outfile]]
93
Canonically label a file of graphs or digraphs.

-s
-g
-z
-S
-t

force output to digraph6 format
If neither -s, -g or -z are given, the output format is
format of the first input graph. As an exception, digraphs
are always written in digraph6 format.
Use sparse representation internally.
Note that this changes the canonical labelling.
Multiple edges are not supported. One loop per vertex is ok.
Use Traces.
Multiple edges and loops are not supported, nor invariants.
-C# Make an invariant in 0..#-1 and output the number of graphs

with each value of the invariant. Dont write graphs unless
-W too.
-W# (requires -C) Output the graphs with this invariant value,
in their original labelling. Dont write the table.
-fxxx Specify a partition of the point set. xxx is any
string of ASCII characters except nul. This string is
considered extended to infinity on the right with the
character z. One character is associated with each point,
in the order given. The labelling used obeys these rules:
(1) the new order of the points is such that the associated
characters are in ASCII ascending order
(2) if two graphs are labelled using the same string xxx,
the output graphs are identical iff there is an
associated-character-preserving isomorphism between them.
No option can be concatenated to the right of -f.
-i#
select an invariant (1 = twopaths, 2 = adjtriang(K), 3 = triples,

4 = quadruples, 5 = celltrips, 6 = cellquads, 7 = cellquins,
8 = distances(K), 9 = indsets(K), 10 = cliques(K), 11 = cellcliq(K),
12 = cellind(K), 13 = adjacencies, 14 = cellfano, 15 = cellfano2,
16 = refinvar(K))
-I#:# select mininvarlevel and maxinvarlevel (default 1:1)
-K#
select invararg (default 3)
-q
===== linegraphg ======================================================
94
Usage: linegraphg [-t] [-q] [infile [outfile]]

Take the linegraphs of a file of graphs.
Input graphs with no edges produce only a warning message.
-t
-q
make the total graph

===== listg ======================================================

Usage: listg [-fp#:#l#o#Ftq] [-a|-A|-c|-d|-e|-H|-M|-s|-b|-G|-y|-Yxxx] [infile [outfile]]
Write graphs in human-readable format.
-f
: assume inputs have same size (only used from a file

and only if -p is given)
-p#, -p#:#, -p#-# : only display one graph or a sequence of
graphs. The first graph is number 1. A second number
which is empty or zero means infinity.
This option wont work for incremental input.
-a : write as adjacency matrix, not as list of adjacencies
-A : same as -a with a space between entries
-l# : specify screen width limit (default 78, 0 means no limit)
This is not currently implemented with -a or -A.
-o# : specify number of first vertex (default is 0).
-d : write output to satisfy dreadnaut
-c : write ascii form with minimal line-breaks
-e : write a list of edges, preceded by the order and the
number of edges
-H : write in HCP operations research format
-M : write in Magma format
-W : write matrix in Maple format
-b : write in Bliss format
-G : write in GRAPE format
-y : write in dot file format
-Yxxx : extra dotty commands for dot files (arg continues to end of param)
-t : write upper triangle only (affects -a, -A, -d and default)
-s : write only the numbers of vertices and edges
-F : write a form-feed after each graph except the last
-q : suppress auxiliary output
-a, -A, -c, -d, -M, -W, -H and -e are incompatible.
===== multig ======================================================
95
Usage: multig [-q] [-u|-T|-G|-A|-B] [-e#|-e#:#]

[-m#] [-f#] [-D#|-r#|-l#] [infile [outfile]]
Read undirected loop-free graphs and replace their edges with multiple
edges in all possible ways (multiplicity at least 1).
Isomorphic multigraphs derived from the same input are suppressed.
-e# | -e#:#
specify a value or range of the total number of edges

counting multiplicities
-m# maximum edge multiplicity (minimum is 1)
-D# upper bound on maximum degree
-r# make regular of specified degree (incompatible with -l, -D, -e)
-l# make regular multigraphs with multiloops, degree #
(incompatible with -r, -D, -e)
Either -l, -r, -D, -e or -m with a finite maximum must be given
-f# Use the group that fixes the first # vertices setwise
-T use a simple text output format (nv ne {v1 v2 mult})
-G like -T but includes group size as third item (if less than 10^10)
The group size does not include exchange of isolated vertices.
-A write as the upper triangle of an adjacency matrix, row by row,
including the diagonal, and preceded by the number of vertices
-B write as an integer matrix preceded by the number of rows and
number of columns, where -f determines the number of rows
-u no output, just count them
-q suppress auxiliary information
===== newedgeg ======================================================
Usage: newedgeg [-lq] [infile [outfile]]
For each pair of non-adjacent edges, output the graph obtained
by subdividing the edges and joining the new vertices.
-l
-q

===== NRswitchg ======================================================

Usage: NRswitchg [-lq] [infile [outfile]]
For each v, complement the edges from N(v) to V(G)-N(v)-v.
-l
Canonically label outputs.
96
-q
===== pickg ======================================================

Usage: [pickg|countg] [-fp#:#q -V] [--keys] [-constraints -v] [ifile [ofile]]
countg : Count graphs according to their properties.
pickg : Select graphs according to their properties.
ifile, ofile : Input and output files.
- and missing names imply stdin and stdout.
Miscellaneous switches:
-p# -p#:#
May fail if input is incremental.
-f
With -p, assume input lines of fixed length
(only used with a file in graph6/digraph6 format)
-v
Negate all constraints
-V
List properties of every input matching constraints.
-l
Put a blank line whenever the first parameter changes,
if there are at least two parameters.
-q
Suppress informative output.
Constraints:
Numerical constraints (shown here with following #) can take
a single integer value, or a range like #:#, #:, or :#. Each
can also be preceded by ~, which negates it.
(For example,
-~D2:4 will match any maximum degree which is _not_ 2, 3, or 4.)
Constraints are applied to all input graphs, and only those
which match all constraints are counted or selected.
-n#
-L#
-d#
-m#
-u#
-s#
-r
-z#
-g#
-T#
-B#
-H#
-E
-a#
-c#
-i#
-j#
number of vertices
-e# number of edges
number of loops
-C
strongly connected
minimum (out-)degree
-D# maximum (out-)degree
vertices of min (out-)degree -M# vertices of max (out-)degree
minimum (in-)degree
-U# maximum (in-)degree
vertices of min (out-)degree -S# vertices of max (out-)degree
regular
-b
bipartite
radius
-Z# diameter
girth (0=acyclic)
-Y# total number of cycles
number of triangles
-K# number of maximal cliques
smallest side of some bipartition (0 if none)
number of induced cycles
Eulerian (all degrees are even, connectivity not required)
group size -o# orbits -F# fixed points -t vertex-transitive
connectivity (only implemented for 0,1,2).
min common nbrs of adjacent vertices;
-I# maximum
min common nbrs of non-adjacent vertices; -J# maximum
97
Sort keys:
Counts are made for all graphs passing the constraints. Counts
are given separately for each combination of values occurring for
the properties listed as sort keys. A sort key is introduced by
-- and uses one of the letters known as constraints. These can
be combined: --n --e --r is the same as --ne --r and --ner.
The order of sort keys is significant.
The output format matches the input, except that sparse6 is used
to output an incremental graph whose predecessor is not output.
===== planarg ======================================================
Usage: planarg [-v] [-nVq] [-p|-u] [infile [outfile]]
For each input, write to output if planar.
-v
-V
-u
-p
-k
-n
-q
Write non-planar graphs instead of planar graphs

Write report on every input
Dont write anything, just count
Write in planar_code if planar (without -p, same format as input)
Follow each non-planar output with an obstruction in sparse6
format (implies -v, incompatible with -p)
Suppress checking of the result
This program permits multiple edges and loops

===== ranlabg ======================================================
Usage: ranlabg [-q] [-f#] [-S#] [infile [outfile]]
Randomly relabel graphs.
Each graph is written in the same format as it is read.
-f# Dont relabel the first # vertices.
-m# Output # randomly labelled copies of each input (default 1).
-S# Set random number seed (taken from clock otherwise).
-q
===== shortg ======================================================

Usage: shortg [-qvkdu] [-i# -I#:# -K#] [-fxxx] [-S|-t] [-Tdir] [infile [outfile]]
98
Remove isomorphs from a file of graphs.

If outfile is omitted, it is taken to be the same as infile
If both infile and outfile are omitted, input will be taken
from stdin and written to stdout
-s
-g
-z
-S
-t

force output to digraph6 format
If none of -s, -z, -g are given, the output format is determined
by the header or, if there is none, by the format of the first
input graph. The output format determines the sorting order too.
As an exception, digraphs are always written in digraph6 format.
Use sparse representation internally. Note that this changes the
canonical labelling.
Multiple edges are not supported. One loop per vertex is ok.
Use Traces.
Multiple edges,loops, directed edges are not supported,
nor invariants.
-k
output graphs have the same labelling and format as the inputs.
Without -k, output graphs have canonical labelling.
-s, -g, -z are ineffective if -k is given.
-v
write to stderr a list of which input graphs correspond to which

output graphs. The input and output graphs are both numbered
beginning at 1. A line like
23 : 30 154 78
means that inputs 30, 154 and 78 were isomorphic, and produced
output 23.
-d
include in the output only those inputs which are isomorphic

to another input. If -k is specified, all such inputs are
included in their original labelling. Without -k, only one
member of each nontrivial isomorphism class is written,
with canonical labelling.
-fxxx Specify a partition of the point set. xxx is any

string of ASCII characters except nul. This string is
considered extended to infinity on the right with the
character z. One character is associated with each point,
in the order given. The labelling used obeys these rules:
(1) the new order of the points is such that the associated
characters are in ASCII ascending order
99
(2) if two graphs are labelled using the same string xxx,
the output graphs are identical iff there is an
associated-character-preserving isomorphism between them.
-i# select an invariant (1 = twopaths, 2 = adjtriang(K), 3 = triples,
4 = quadruples, 5 = celltrips, 6 = cellquads, 7 = cellquins,
8 = distances(K), 9 = indsets(K), 10 = cliques(K), 11 = cellcliq(K),
12 = cellind(K), 13 = adjacencies, 14 = cellfano, 15 = cellfano2,
16 = refinvar(K))
-I#:# select mininvarlevel and maxinvarlevel (default 1:1)
-K#
select invararg (default 3)
-u
Write no output, just report how many graphs it would have output.
In this case, outfile is not permitted.
-Tdir Specify that directory "dir" will be used for temporary disk
space by the sort subprocess. The default is usually /tmp.
-q Suppress auxiliary output
===== showg ======================================================

Usage: showg [-p#:#l#o#Ftq] [-a|-A|-c|-d|-e] [infile [outfile]]
Write graphs in human-readable format.
infile is the input file in graph6 or sparse6 format
outfile is the output file
Defaults are standard input and standard output.
-p#, -p#:#, -p#-# : only display one graph or a sequence of
graphs. The first graph is number 1. A second number
which is empty or zero means infinity.
-a
-A
-d
-c
-e
:
:
:
:
:
-o#
-t
-F
-l#
:
:
:
:
-q
write the adjacency matrix

same as -a with a space between entries
write output to satisfy dreadnaut
write compact dreadnaut form with minimal line-breaks
write a list of edges, preceded by the order and the
number of edges
specify number of first vertex (default is 0)

write upper triangle only (affects -a, -A, -d and default)
write a form-feed after each graph except the last
specify screen width limit (default 78, 0 means no limit)
This is not currently implemented with -a or -A.
-a, -A, -c, -d and -e are incompatible.

===== subdivideg ======================================================
100
Usage: subdivideg [-k#] [-q] [infile [outfile]]

Make the subdivision graphs of a file of graphs.
-k# Subdivide each edge by # new vertices (default 1)
-q
===== twohamg ======================================================

Usage: twohamg [-sgvq] [-L#] [infile [outfile]]
Partition quartic graphs into two hamiltonian cycles.
Output those which cannot be partitioned.
-s
-g

If neither -s or -g are given, the output format is
format of the first input graph. Also see -S.
-p
Read a cubic graph and use its prism. Vertex i of the input becomes
vertices 2*i,2*i+1 in the prism.
-x Test for decompositions using each 2-path
-X As -x but only output if two 2-paths are missed at some vertex
-y Test for decompositions using each non-triangular 3-path
-t# With -x and -X, consider only paths with center #
With -y, consider only paths starting at #
-Y With -p, only consider paths whose central edge is vertical
-v Give a partition for those graphs who have one and a message
for those which dont. With -x, list exceptional 2-paths.
-L# Limit to 1000*# iterations; write with message if timeout.
Graphs that time out are written to the output.
-q
===== vcolg ======================================================

Usage: vcolg [-q] [-u|-T|-G|-A|-B] [-e#|-e#:#]
[-m#] [-f#] [-D#|-r#|-l#] [infile [outfile]]
Read undirected loop-free graphs and colour their vertices in
in all possible ways with colours 0,1,2,... .
Isomorphic graphs derived from the same input are suppressed.
101
-e#
-m#
-f#
-T
-u
-q
| -e#:# specify a value or range of the total value of the colours

number of available colours (default 2)
Use the group that fixes the first # vertices setwise
use a simple text output format (nv ne {col} {v1 v2})
no output, just count them
===== watercluster2 ======================================================

usage: watercluster2 [ix] [oy] [m] [T] [C] [B] [S] .
The option ix restricts the maximum indegree to x.
The option oy restricts the maximum outdegree to y.
The default maximum in- and out-degrees are unlimited.
T means: Output directed graphs in T-code -- for details see header
B means: Output directed graphs in binary code -- for details see header
C means: Do really construct all the directed graphs in memory, but dont output them.
S means that for each edge only one direction must be chosen -- not both.
Default is that both are allowed
-- so the edge a-b can become a->b AND b->a in the same output graph.
m means: read multicode instead of g6 code
102
References
[1] J. M. Boyer and W. J. Myrvold, On the cutting edge: simplified O(n) planarity by
edge addition, J. Graph Alg. Appl., 8 (2004) 241273.
[2] P. T. Darga, M. H. Liffiton, K. A. Sakallah, and I. L. Markov, Exploiting Structure in
Symmetry Generation for CNF, Proceedings of the 41st Design Automation Conference, 2004, 530534. Source code at http://vlsicad.eecs.umich.edu/BK/SAUCY.
[3] B. D. McKay, Hadamard equivalence via graph isomorphism, Discrete Math., 27
(1979) 213214.
[4] A. Kirk, Efficiency considerations in the canonical labelling of graphs, Technical
report TR-CS-85-05, Computer Science Department, Australian National University
(1985).
[5] B. D. McKay, A. Meynert and W. Myrvold, Small Latin squares, quasigroups and
loops, J. Combin. Designs, to appear.
[6] T. Miyazaki, The complexity of McKays canonical labelling algorithm, in Groups
and Computation, II, DIMACS Ser. Discrete Math. Theoret. Comput. Sci., 28, Amer.
Math. Soc. (1997) 239256.
[7] K. E. Malysiak, Graph Isomorphism, Canonical Labelling and Invariants, Honours
Thesis, Computer Science Department, Australian National University (1987).
[8] R. Mathon, Sample graphs for isomorphism testing, Congressus Numerantium, 21
(1978) 499517.
[9] B. D. McKay, Practical graph isomorphism, Congressus Numerantium, 30 (1981)
4587. Available at http://cs.anu.edu.au/bdm/nauty/PGI.
[10] B. D. McKay and Adolfo Piperno, Practical graph isomorphism II, J. Symbolic Comput., 60 (2014) 94112.
103

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nauty and Traces Users Guide (Version 2.

Research School of Computer Science

August 19, 2016

How to use this Guide.

How to use this Guide

An automorphism of a graph is a permutation of the vertex labels so that the set of

(0 6)(1 7)(2 4)(3 5)

Because the number of automorphisms can be extremely large, it is more efficient to

The purpose of canonical labelling is to test isomorphism: two isomorphic graphs

(A) Commands that set the mode.

Ad+,As+,At+ As well as changing the mode, if g is defined it is converted to the data

Set value of n. The maximum value depends on available memory.

Read the graph g.

r . . . ; Relabel the graph g, where . . . is a permutation of {0, 1, . . . , n1}, specifying

Relabel the graph g in order of the partition , and permute consistently.

reduced and relabelled consistently.

Relabel the graph g at random. The partition is permuted consistently.

(C) Commands which define the partition .

Perform a refinement operation, replacing the partition by its refinement. The

Perform a refinement operation, an application of the vertex-invariant (if one has

(D) Commands which establish or examine options.

Establish an origin for vertex numbering. The default is 0. Only non-negative

Ignored. Provided for contrast with -.

Set option writeautoms to TRUE or FALSE, respectively. This tells nauty or

Set option writemarkers to TRUE or FALSE, respectively. This tells nauty

Set option cartesian to TRUE or FALSE, respectively. This tells nauty or

Set a parameter that effects a probabilistic method (random Schreier algorithm).

Specify a strategy for Traces. Only 0 is supported in this version.

Select a vertex-invariant. One user-defined vertex-invariant can be linked with

Request calls to user-defined functions (nauty only). The value is

Type the current partition , unless it is has only one cell.

= (V0 , V1 , . . . , Vm ) and let vi be the least numbered vertex in Vi for 0 i m.

Execute nauty or Traces. The program to execute depends on the mode.

Copy h, if defined, to h0 . See the description of the # command for more.

Help: type a summary of dreadnaut commands.

Flush the output file.

(G) Command line options

Sample dreadnaut sessions

h and h are identical.

the relabelled graph

int d: pointer to an array of length at least nv

The orbits of the automorphism group is also represented by an array of n integers,

is the permutation (0 2 5)(1 3 6 4)

gives the orbits {0, 1, 4, 5}, {2, 3, 7}, {6, 8}

A colouring (partition) of the vertices is specified by a pair of arrays, usually called

all vertices in some order

cells end where the zeros are

all vertices in some order

cells end where the zeros are

Options and statistics

is written can be found in Section 8. Default FALSE (but dreadnaut sets it to

The default is adjacencies for DEFAULTOPTIONS DIGRAPH, adjacencies sg

int numgenerators: The number of generators found.

unsigned long numnodes: The total number of tree nodes generated.

Calling nauty and Traces

Low level nauty calls

nauty. This argument is ignored if options.getcanon = FALSE, in which case

always internally numbered 0, 1, . . . , n1. By default, k = 0. Only non-negative values

Interpretation of the output