Installing and Using Phylogentics Software: ClustalX, PHYLIP, TreeView

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Ta#le of Contents
Obtaining the Software........................................................................................................ 2 Installing the Software......................................................................................................... 2 ClustalX...........................................................................................................................2 PHYLIP...........................................................................................................................3 TreeView.........................................................................................................................3 Running the Software.......................................................................................................... !ligning se"uen#es with ClustalX.................................................................................. Viewing tree files with TreeView................................................................................. $2 %sing PHYLIP.............................................................................................................. $3 &or'ing fro( the #o((an) *ro(*t........................................................................$+ Running PHYLIP *rogra(s..................................................................................... $ ,-a(*le $ . /eighbor01oining 2etho).............................................................. $3 ,-a(*le 2 . 4ootstra* Ran)o( Sa(*ling5 2a-i(u( Parsi(on65 7 Consensus Tree...................................................................................................................... 2$

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Installing and Using Phylogentics Software: ClustalX, PHYLIP, TreeView

(Windows) $#taining the Software The software is obtained from three sources: ClustalX http://www igbmc.u strasbg.fr/!io"nfo/ClustalX/ #$%&"# http://e'olution.genetics.washington.edu/ph(lip.html Tree)iew http://ta*onom(.+oolog(.gla.ac.u,/rod/tree'iew.html "ncluded with this tutorial are the current 'ersions (ClustalX 1.-./ #$%&"# ..0./ 1 Tree)iew 1.0.0)/ as of 2ebruar( 13/ 4556/ in three self e*tracting 7"# files. Installing the Software 2irst/ cop( the three self e*tracting 7"# files to the Windows 8es,top. ClustalX (89: 1 protein se;uence alignment software): &ocate the self e*tracting 7"# file (ClustalX %&'(&e)e) 8ouble clic, to open the file and (ou will see . . .

The default director(/folder where the ClustalX files will be e*tracted to is the <root= director(. That is most li,el( on dri'e C. "t is e*tracted into a folder called ClustalX (so (ou don>t ha'e to worr( about a whole pile of files being e*tracted to the root director( in a
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disorgani+ed wa(). "f (ou want the program (and all its associated files) to be e*tracted to another location (ou can indicate that b( either t(ping it in directl( or using the *rowse&&& button. Once (ou ha'e selected the destination director( for files to be e*tracted into simpl( clic, the Un+i, button. : final confirmation message will pop up when e*traction is finished and (ou can clic, $-. :lso clic, the Close button of the <Win7ip ?elf @*tractor= window.

#$%&"# (distance matri* calculation/ tree building/ 1 tree 'iewing): &ocate the self e*tracting 7"# file. (Phyli, (&.(&e)e) 8ouble clic, to open the file and (ou will see . . .

The default director(/folder where the #$%&"# files will be e*tracted to is the <root= director(. That is most li,el( on dri'e C. "t is e*tracted into a folder called #h(lip (so (ou don>t ha'e to worr( about a whole pile of files being e*tracted to the root director( in a disorgani+ed wa(). "f (ou want the program (and all its associated files) to be e*tracted to another location (ou can indicate that b( either t(ping it in directl( or using the *rowse&&& button. Once (ou ha'e selected the destination director( for files to be e*tracted into simpl( clic, the Un+i, button. : final confirmation message will pop up when e*traction is finished and (ou can clic, $-. :lso clic, the Close button of the <Win7ip ?elf @*tractor= window.

Tree)iew (tree 'iewing/ printing/ and rearrangement): &ocate the self e*tracting 7"# file (TreeView %&.&.&e)e) 8ouble clic, to open the file and (ou will see . . . The default director(/folder where the Tree)iew files will be e*tracted to is is a new subdirector( on the des,top called Tree)iew .
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(assuming the self e*tracting file is run from the 8es,top). This software differs from the pre'ious installed since it actuall( adds a menu item to the Progra/s list (under Start) and b( default places itself in the Progra/ 0iles director(. Once (ou ha'e selected the destination director( for files to be e*tracted into simpl( clic, the Un+i, button. : final confirmation message will pop up when e*traction is finished and (ou can clic, $-. :lso clic, the Close button of the <Win7ip ?elf @*tractor= window. The newl( e*tracted files now need to be installed b( running the S1TUP&1X1 program in the Tree)iew director(/folder.

8ouble clic, the S1TUP&1X1 program to run it and (ou will see the program begin setting up. "t will loo, li,e this. . . . The ne*t screen will loo, li,e the following and instructs (ou to shut down all other programs before continuing.

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Clic, 2e)t to continue. : username and compan( now has to be entered before installation can continue.

Once entered clic, 2e)t to continue. The ne*t screen allows (ou to change the installation director(/folder to something other than the default. $a'ing decided on an installation location clic, 2e)t to continue.

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:nother window opens indicating the location and name of the Tree)iew folder in the #rograms list.

"f e'er(thing meets with (our appro'al clic, 2e)t to continue. : window will then open indicating all selections made.

"f e'er(thing loo,s good/ once again/ clic, 2e)t to continue. #rogress of installation will be displa(ed and a final window will tell (ou to clic, 0inish to complete the installation.

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3unning the Software O'er'iew: The maBor steps in using these programs for ph(logenetic anal(ses are . . . :lign 89: or protein se;uences C ClustalX Desample the aligned se;uences (if bootstrapping/ Bac, ,nifing/ etc. is desired) C various PHYLIP software Compute distance matrices (if distance methods of tree building are to be used) C various PHYLIP software Dun tree building software C various PHYLIP software Construct a consensus tree (if multiple data sets/samples were used in tree building) C various PHYLIP software Compute distances between trees (if multiple trees ha'e been constructed) C various PHYLIP software )iew and print tree(s) C TreeView 4ligning se5uences with ClustalX: 2irst/ information is needed to align. One relati'el( eas( method of accessing se;uence data is through 9C!" (9ational Center for !iotechnolog( "nformation): http://www.ncbi.nlm.nih.go'/ To easil( find se;uences that are related (ou can perform a nucleotide search using terms li,e <iguania 9:8$ subunit 1=. The following e*amples used here were obtained from the search results and include 1A of the Liolaemus sp. listed.

?ince one of the file formats ClustalX can easil( read in is 2:?T: the 9C!" results can be displa(ed in the 2:?T: format and then copied and pasted to a te*t file.

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?e;uences to be aligned are often placed in the same file. One of the easiest wa( to do this is to open 2ote,ad and cop( information from the 2:?T: format on the web page and paste it into a new te*t file. To run
2ote,ad clic, on the Start button on the 8es,top and then clic, 3un&&& : window will open were (ou can t(pe in note,ad and then clic, $6.

2rom the 9C!" web page (with the se;uence information in 2:?T: format) select the te*t to be copied using the mouse and ensuring to include the initial 7 that is used b( ClustalX to recogni+e 2:?T: data.

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#robabl( the easiest wa( to cop( and paste the te*t is to highlight the data with the mouse and then use Ctrl8C (holding the Ctrl ,e( while at the same time pressing C) to cop( the selected te*t from the web page and then switch to the 2ote,ad program window and use Ctrl8V to paste the copied information. (I/,ortant9 Once the information is pasted (ou will need to press 1nter at least once to mo'e to the ne*t line where the ne*t string of data will be pasted.) :lso/ if (ou would li,e the se;uences to be listed b( something other than the Een!an, "8 (ou will need to edit what comes right after the 7 on the first line of a se;uence/ such as from . . . >gi|55924993|gb|AY661907.1| Liolaemus sarmientoi NAD To . . . >sarmientoi . . .

2ote: 9ames will be cut at 15 characters when aligned se;uences are e*ported for use b( #$%&"#. To start ClustalX (assuming it was installed as listed abo'e) find the program and run it. @'er(thing it needs to run is in its director(/folder. $ere is one wa( to get to the program. . . . Open :y Co/,uter (located on the 8es,top) Eo to the root director( of dri'e C to find the ClustalX director(/folder. To get to the root director( simpl( double clic, on the dri'e C in this case C43T138L4* C:"

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The ne*t 'iew will loo, something li,e below and (ou can double clic, on the ClustalX folder to open it.

"nside the ClustalX folder (ou will find the program icon and name loo,ing something li,e this: 8ouble clic, the program to open and run it. (2$T1: %ou ma( want to create a <shortcut= to ma,e it easier to access the program later. To do this simpl( right clic, the program file once and choose Create Shortcut from the menu. 2or eas( access cut and paste Gusing the menu accessed b( right clic,ingH the newl( created shortcut onto the 8es,top or some other easil( accessible location.)

Ian( adBustments can be made in ClustalX that will affect alignment. The Hel, pro'ided b( the software is e*tensi'e and detailed. "n the following e*ample default 'alues will be used. :lignment of the e*ample se;uences is done b( . . . &oad the se;uences (0ile C Load Se5uences) from the te*t file created (Li+ards&t)t in this e*ample). 2ote: The $,en window will alwa(s begin in the ClustalX director(/folder/ so (ou will ha'e to na'igate around to the file location. :lso/ output files will (b( default) be sa'ed in the same location as the input file/ onl( with different e*tensions (.dnd/ .ph(/ .ph/ aln/ . . .). 2ote: "t is at this point prior to beginning alignment where (ou can change the alignment parameters (4lign/ent C 4lign/ent Para/eters).

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?et the output format to include #$%&"# (4lign/ent C $ut,ut 0or/at $,tions C place a chec, beside PHYLIP for/at C Close). #erform a <complete alignment= to get started (4lign/ent C ;o Co/,lete 4lign/ent). !efore alignment begins (ou are gi'en the opportunit( to gi'e the output files different names from the default ones (which consist of the original file name with new e*tensions).

"f the e*ample data were used the ClustalX window will now loo, li,e this:

@*amination of the aligned se;uences is now recommended. $owe'er/ editing will ha'e to be done from within a sa'ed se;uence file. (ClustalX se;uence format files are easier to 'iew and edit/ since the( ha'e labels for each row and ha'e columns of all matching se;uences mar,ed/ while #$%&"# format se;uence files
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contain labels onl( on the first set of rows and ha'e no e*tra mar,ings.) To edit a file open 2ote,ad (Start C 3un&&& C @nter note,ad and clic, $6) and then find and open (0ile C $,en&&& C 0iles of ty,e: C 4ll 0iles Gsince files sa'ed b( ClustalX with default names do not ha'e the e*tension &t)t and would therefore not appear in the folders 'iewedH) and edit the file from there. (2ote: ?ome old 'ersions of 2ote,ad ma( alwa(s add the e*tension &t)t to the end of a sa'ed file.) :s an e*ample (ou could open and edit the default Li+ards&aln file created during se;uence alignment. ClustalX se;uence files cannot be read b( #$%&"# so if (ou edit a ClustalX formatted file (ou will need to load in the edited file and sa'e it in #$%&"# format. &oad in edited ClustalX se;uence file (0ile C Load Se5uences C then find the edited &aln file). ?a'e the se;uence in #$%&"# format (0ile C Sa<e Se5uences as&&& C select #$%&"# under 0or/at and then clic, $6). : 9eighbor Joining tree can be easil( constructed in ClustalX. Once the se;uences ha'e been aligned (or after (ou ha'e loaded in some aligned se;uences) draw a 9eighbor Joining tree using Trees C ;raw 28= Tree. %ou are gi'en the option of pro'iding a new name for the tree file.

Viewing tree files with TreeView: Dight now (ou would probabl( li,e to see an actual tree in a format other than this default #$%&"# output format used b( ClustalX: !!sarmientoi"0.01523#gallar$oi"0.01213%"0.00345#!&ull'i "0.00515#ar()e*orus"0.005+1%"0.006+3#!!tari"0.00667#bag uali"0.00633%"0.02006#!!)at()eri"0.03269#sil,anae"0.047 04%"0.00796#!!!!-ant)o,iri$is"0.00+13#(an.ueli"0.01606% "0.01116#melano/s"0.01743%"0.01639#$onosobarrosi"0.031+ 5%"0.03334#!0riegi"0.0250+#elongatus"0.02460%"0.07951%" 0.02271%"0.03013%"0.00765%1 "f Tree)iew was installed as listed abo'e #$%&"# tree format file e*tensions should be associated with Tree)iew and the trees can be opened b( double clic,ing the tree file (Li+ards&,h in this e*ample). "f that isn>t the case (ou can start Tree)iew b( going to Start C Proga/ 0iles C TreeView. 2rom within Tree)iew tree files can be opened for 'iewing 14
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using 0ile C $,en&&& Tree)iew has four different tree 'iewing formats. ?electing a particular format is as simple as clic,ing the button: The following screen shot shows the same tree in all four formats:

Trees can be printed (0ile C Print&&&) or e*ported as graphics files (0ile C Sa<e as gra,hic&&&). :lso/ if the need e'er arises/ trees can be completel( rearranged (1dit C 1dit tree). Using PHYLIP: #$%&"# is a collection of indi'idual programs written to perform specific calculations. One program often produces output (in the form of a file) (ou will use in another #$%&"# program for further anal(sis. There are some default input file names used or searched for when a #$%&"# program is started (<infile=)/ but it is recommended that more descripti'e names be used that are less li,el( to lead to confusion (especiall( when man( different tests are run). 8efault output files are generall( <outfile= or <outtree=. Once (ou get used to it the most efficient wa( to run #$%&"# 1.
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program is from the command prompt. Ksing the command prompt window an( errors reported can be obser'ed as well as information about final output. ("f programs are run b( double clic,ing from within the #h(lip director(/folder errors and final output messages ma( not be seen C since once the program finishes running the window immediatel( closes.) To wor, from the command prompt a few commands need to be re'iewed. Wor,ing from the command prompt To get to the command prompt clic, on Start C 3un&&& C t(pe co//and C clic, $6 (or press 1nter). : window similar to below will open.

The information to the left of the 7 indicates the director(/folder that is currentl( immediatel( accessible. To switch to the #$%&"# director(/folder t(pe in: cd >Phyli, The information to the left of the 7 should now read <C:>PHYLIP=. This indicates that (ou are now wor,ing on hard dri'e C within the director( #$%&"#. 9ow it would be nice to see what is in that director(. To list the contents of the director( t(pe in: dir "f all has gone well so far the window will displa( something similar below.

1A

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%ou will notice that there are three more directories (subdirectories) listed within the #$%&"# director( (ou are now in. The three directories are doc/ e)e/ and src. These directories contain the #$%&"# documentation files/ e*ecutable programs/ and program source code respecti'el(. There are also two files in the #$%&"# director(. Phyli,&ht/l is documentation in $TI& format 'iewed with a web browser and ,hyli,?&,df is a <primer= written b( a user (not the #$%&"# pac,age creator) that is 'er( useful. (The <primer= is highl( recommended reading. Once it has been read the more detailed contents of the #$%&"# documentation written b( the original author will fall into place more easil(.) To access the documents locate the files b( double clic,ing on :y Co/,uter on the Windows des,top and na'igating to the #$%&"# director(/folder (probabl( dri'e C and director(/folder #h(lip). 8ouble clic, the files to open them with the associated programs (most li,el( "nternet @*plorer and :dobe :crobat Deader). 8irector( e)e contains the #$%&"# programs. To switch to the e)e director( t(pe: cd e)e To list the files within the director( t(pe: dir 2ote: %ou can also change to the director( with the e*ecutable #$%&"# programs in it using a single command once the command window is opened: cd >Phyli,>e)e

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%ou will notice that man( of the files listed scroll off the top of the window. The( can be 'iewed b( using the scroll bar on the right side of the window to loo, bac, up the list. :nother wa( to 'iew more of the files in the director( is to acti'ate a <switch= for the dir command. "n order to 'iew a more compact director( listing t(pe in: dir @w

:ll the indi'idual #$%&"# programs are now 'isible. To run a program simpl( t(pe its name. There are a few more commands that will be useful: co,y (e*. co,y outfile dataout): copies the contents of one file (outfile) to another and gi'es it a new name (dataout) rena/e (e*. rena/e outfile dataout): renames a file (outfile) with a new name (dataout) 10
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del (e*. del outfile): deletes a file (outfile)

: summar( of commands discussed abo'e that are useful when using #$%&"# programs is presented in the table below.
Command cd dir dir @w co,y rena/e del e)it Example cd >Phyli,>e)e dir dir @w Function Change to the listed director( &ist director( contents &ist director( contents in wide format Cop( a file and gi'e it a new name co,y outfile dataout rena/e outfile dataout Dename a file 8elete/remo'e a file del outfile @*it/close the command window e)it

When (ou are finished wor,ing within the command prompt window (ou can most easil( close the window b( t(ping: e)it "f (ou use the mouse to close the window (using the X in the top right corner) (ou will li,el( recei'e an additional prompt or error message. "f (ou reall( do want to close the window clic, the 1nd 2ow button. Dunning #$%&"# programs "n order to anal(+e aligned se;uences using #$%&"# programs multiple programs ha'e to be run se;uentiall(. :t this point it is important to (once again) repeat how important reading the <primer= in #82 format and the #$%&"# complete documentation is. There are two specific pages in the <primer= (,hyli,?&,df in the #$%&"# director(/folder) that clarif( much of the confusion that initiall( surrounds use of the programs. #age 6. lists in a table the categories of data each program is used for and page 6A shows the flow or se;uence of data being processed using multiple programs (from aligned se;uences up to tree 'iewing). !elow are two e*amples of the process. Complete descriptions of all options for each program are not pro'ided. The full #$%&"# documentation describes the 'arious settings and switches for each of the program thoroughl(. Iost of the commonl( used options are mentioned in the <primer=.

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Example 1

!ei"#$or%&oinin" 'et#od

?tep 1: #lace the aligned se;uence data file into #$%&"#>s director(. 2ind the te*t file containing the aligned se;uence data (Li+ards&,hy in this e*ample) and use cop( (right clic, and Co,y or Ctrl8c). #aste (right clic, and Paste or Ctrl8<) to put it into the e)e director(. (Kse :y Co/,uter on the Windows des,top to locate the director( Phyli, and subdirector( e)e and paste the copied file in the e)e director( C C:L#h(lipLe*e) ?tep 4: Eo to the command prompt within the Phyli, director(. Clic, Start and then 3un&&& on the Windows des,top. T(pe in co//and and press 1nter or clic, $6. Change to the #$%&"# director( containing the e*ecutable programs b( t(ping in: cd >Phyli,>e)e and pressing 1nter. ?tep .: Dun the distance matri* calculation program/ dnadist. T(pe dnadist or dnadist&e)e and press 1nter.

?ince the se;uence containing te*t file is not named infile the name of the file to use must be t(ped in. Li+ards&,hy is used in this e*ample.

2ote: "f at an( time (ou want to stop the program (ou can use Ctrl8c to e*it the program and return to the command prompt.

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"f all is well the screen 'iew abo'e will appear. . . . To accept the default settings listed on the menu and continue processing press Y. "f (ou want to change a setting listed on the menu press the letter associated with it. (@*. #ress ; to choose a different e'olutionar( model used in calculations.)

The screen abo'e will be 'isible when processing is complete. "t indicates that data calculated has been written to the file named outfile. Dename outfile. T(pe in: rena/e outfile Li+ards;istance:atri) and press 1nter. ?etp A: Dun the tree building program/ neigh#or. Dun the program for 9eighbor Joining tree calculations b( t(ping: neigh#or and pressing 1nter. 1F
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T(pe in the name of the file containing the distance matri* that was Bust calculated and renamed: Li+ards;istance:atri)

"f all has wor,ed well the 'iew abo'e will be displa(ed. "f all options are set to desired 'alues press Y and 1nter to calculate the tree.

The screen indicates two files were produced. $utfile contains a simple te*t 'iew of the tree produced along with branch lengths. ?tep 6: )iew the output data using 2ote,ad and TreeView. To 'iew outfile (ou can run 2ote,ad and then na'igate to the #$%&"# director( (C:L#h(lipLe*e) and open the file. One method of opening 2ote,ad is b( doing the following: Start C 3un&&& t(pe in note,ad C press 1nter or clic, $6. 2rom within 2ote,ad use 0ile C

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$,en and na'igate to the location of the file to open (C:L#h(lipLe*e). (To list files that do not end with the e*tension .t*t change 0iles of ty,e: to 4ll 0iles.) ?tart Tree)iew for a graphical 'ersion of the tree: Start C Progra/s C TreeView Open the tree file produced b( neigh#or&e)e: 0ile C $,en&&& na'igate to the director( with the outtree file (C:L#h(lipLe*e). "n order to see the file outtree listed set 0iles of ty,e: to 4ll files A&A" ?tep 0: Dename output files. "f more trees are to be created change the name of outtree to something else. "n this e*ample it will be changed to Li+ards2eigh#orTree. To change the file name t(pe: rena/e outtree Li+ards2eigh#orTree To gi'e a new name to outfile t(pe: rena/e outfile Li+ards2eigh#or0ile Example ( )ootstrap *andom +amplin", 'aximum Parsimon-, . Consensus Tree ?tep 1: #lace the aligned se;uence data file into #$%&"#>s director(. 2ind the te*t file containing the aligned se;uence data (Li+ards&,hy in this e*ample) and use cop( (right clic, and Co,y or Ctrl8c). #aste (right clic, and Paste or Ctrl8<) to put it into the e)e director(. (Kse :y Co/,uter on the Windows des,top to locate the director( Phyli, and subdirector( e)e and paste the copied file in the e)e director( C C:L#h(lipLe*e) ?tep 4: Eo to the command prompt within the Phyli, director(. Clic, Start and then 3un&&& on the Windows des,top. T(pe in co//and and press 1nter or clic, $6. Change to the #$%&"# director( containing the e*ecutable programs b( t(ping in: cd >Phyli,>e)e and pressing 1nter. ?tep .: Dun the bootstrapping program/ se5#oot. T(pe se5#oot or se5#oot&e)e and press 1nter. T(pe in the name of the aligned se;uences data file: Li+ards&,hy and press 1nter.

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The menu abo'e will appear if all is functioning properl(. "f all menu settings are set as desired press Y and 1nter. @nter an odd number to use as a random number seed. 2ote: "f there is a file with the same name as the output file (ou will be as,ed whether (ou want to Deplace the file/ :ppend the file/ write a new 2ile/ or Muit. "f (ou choose to write a new file (ou will need to enter a new file name to use for the output file.

?tep A: Dename outfile. Ei'e outfile a new name (so that there is no conflict or dela( with 44
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the output file of the ne*t program. To change outfile to Li+ards*ootstra, t(pe: rena/e outfile Li+ards*ootstra, ?tep 6: Dun the tree building program/ dna,ars. T(pe dna,ars or dna,ars&e)e and press 1nter. T(pe in the name of the file containing bootstrap data/ Li+ards*ootstra, and press 1nter.

Change the settings to anal(+e multiple data sets. T(pe : and 1nter. Iultiple data sets are to be anal(+ed so t(pe ; and 1nter. 155 data sets were sa'ed when se5#oot was run so t(pe %BB and 1nter when it as,s how man( data sets to anal(+e. T(pe in an odd number to use as a random number seed. T(pe in how man( times it should Bumble (how man( orders/arrangements of species it should run). . . . Tr( 15.

4.

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: menu similar to abo'e should appear after the entries ha'e been made. When menu items are set the wa( (ou want t(pe Y and press 1nter.

The screen indicates two files were produced. $utfile contains a simple te*t 'iew of the tree produced along with branch lengths. ?tep 0: Dename the output files. Dename outfile to Li+ards*ootPars. T(pe rena/e outfile Li+ards*ootPars and press 1nter. Dename outtree to Li+ards*ootTrees. T(pe rena/e outtree Li+ards*ootTrees and press 1nter. ?tep 3: Dun the consensus tree building program/ consense. T(pe in consense or consense&e)e and press 1nter. T(pe in the name of the data file containing the 'arious trees:

4A

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Li+ards*ootTrees and press 1nter.

Change options listed on the menu if desired then t(pe Y and press 1nter to start processing. 9otification of two output files (outtree and outfile) is gi'en. ?tep -: )iew the output data using 2ote,ad and TreeView. To 'iew outfile (ou can run 2ote,ad and then na'igate to the #$%&"# director( (C:L#h(lipLe*e) and open the file. One method of opening 2ote,ad is b( doing the following: Start C 3un&&& t(pe in note,ad C press 1nter or clic, $6. 2rom within 2ote,ad use 0ile C $,en and na'igate to the location of the file to open (C:L#h(lipLe*e). (To list files that do not end with the e*tension .t*t change 0iles of ty,e: to 4ll 0iles.) ?tart Tree)iew for a graphical 'ersion of the tree: Start C Progra/s C TreeView Open the tree file produced b( consense&e)e: 0ile C $,en&&& na'igate to the director( with the outtree file (C:L#h(lipLe*e). "n order to see the file outtree listed set 0iles of ty,e: to 4ll files A&A"

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"f unrooted tree format is selected something similar to the 'iew displa(ed abo'e will be shown. &engths of branches indicate how man( times out of the 155 trees e*amined the grouping held true. ?tep 0: Dename output files. "f more trees are to be created change the name of outtree to something else. "n this e*ample it will be changed to Li+ardsConsenseTree. To change the file name t(pe: rena/e outtree Li+ardsConsenseTree To gi'e a new name to outfile t(pe: rena/e outfile Li+ardsConsense0ile

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