Scribd
Upload
29 views

J Model Test

The document describes using jModelTest to determine the best fitting model of nucleotide substitution for a dataset of 10 sequences and 537 sites. jModelTest calculated likelihood scores for 6 substitution models using PhyML and selected SYM+G as the best model according to the Akaike Information Criterion.

Uploaded by

Erika Macas
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as TXT, PDF, TXT or read online on Scribd
29 views

J Model Test

The document describes using jModelTest to determine the best fitting model of nucleotide substitution for a dataset of 10 sequences and 537 sites. jModelTest calculated likelihood scores for 6 substitution models using PhyML and selected SYM+G as the best model according to the Akaike Information Criterion.

Uploaded by

Erika Macas
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as TXT, PDF, TXT or read online on Scribd
You are on page 1/ 3

----------------------------- jModeltest 2.

0 -----------------------------
(c) 2011-onwards Diego Darriba, David Posada,
Department of Biochemistry, Genetics and Immunology
University of Vigo, 36310 Vigo, Spain. e-mail: [email protected], [email protected]
--------------------------------------------------------------------------------
Tue Jun 13 03:36:11 CEST 2023
Linux 4.19.0-16-amd64, arch: amd64, bits: 64, numcores: 12

Citation: Posada D. 2008. jModelTest: Phylogenetic Model Averaging.


Molecular Biology and Evolution 25: 1253-1256.

jModelTest 2.0 Copyright (C) 2011 Diego Darriba, David Posada


This program comes with ABSOLUTELY NO WARRANTY
This is free software, and you are welcome to redistribute it
under certain conditions

Notice: This program may contain errors. Please inspect results carefully.

Arguments = -g 4 -d
/httpd/bioinfo/wum_sessions_v0.7/1279963/jobs/455945/outfile.out -t ML -s 3 -AIC -
tr 2

Reading data file "outfile.out"... OK.


number of sequences: 10
number of sites: 537

---------------------------------------------------------------
* *
* COMPUTATION OF LIKELIHOOD SCORES WITH PHYML *
* *
---------------------------------------------------------------

::Settings::
Phyml version = 3.0
Phyml binary = PhyML_3.0_linux64
Candidate models = 6
number of substitution schemes = 3
including only models with equal base frequencies
including only models without a proportion of invariable sites
including models with/without rate variation among sites (+G) (nCat = 4)
Optimized free parameters (K) = substitution parameters + 17 branch lengths +
topology
Base tree for likelihood calculations = ML tree
Tree topology search operation = NNI
computing likelihood scores for 6 models with Phyml 3.0

::Progress::
Model Exec. Time Total Time -lnL
-------------------------------------------------------------------------
JC 00h:00:04:03 00h:00:04:03 2998.0555
K80 00h:00:03:00 00h:00:07:03 2954.13799
JC+G 00h:00:16:05 00h:00:16:06 2984.99462
SYM 00h:00:02:07 00h:00:19:03 2948.59673
K80+G 00h:00:12:07 00h:00:20:00 2942.36737
SYM+G 00h:00:10:07 00h:00:30:00 2937.9199

Model = JC
partition = 000000
-lnL = 2998.0555
K = 18

Model = JC+G
partition = 000000
-lnL = 2984.9946
K = 19
gamma shape = 1.4290

Model = K80
partition = 010010
-lnL = 2954.1380
K = 19
kappa = 2.6246 (ti/tv = 1.3123)

Model = K80+G
partition = 010010
-lnL = 2942.3674
K = 20
kappa = 2.8760 (ti/tv = 1.4380)
gamma shape = 1.6080

Model = SYM
partition = 012345
-lnL = 2948.5967
K = 23
R(a) [AC] = 0.9120
R(b) [AG] = 2.1860
R(c) [AT] = 1.2069
R(d) [CG] = 1.0490
R(e) [CT] = 3.3349
R(f) [GT] = 1.0000

Model = SYM+G
partition = 012345
-lnL = 2937.9199
K = 24
R(a) [AC] = 0.8848
R(b) [AG] = 2.3388
R(c) [AT] = 1.2427
R(d) [CG] = 1.0313
R(e) [CT] = 3.6436
R(f) [GT] = 1.0000
gamma shape = 1.7630

Computation of likelihood scores completed. It took 00h:00:30:00.

---------------------------------------------------------------
* *
* AKAIKE INFORMATION CRITERION (AIC) *
* *
---------------------------------------------------------------

Model selected:
Model = SYM+G
partition = 012345
-lnL = 2937.9199
K = 24
R(a) [AC] = 0.8848
R(b) [AG] = 2.3388
R(c) [AT] = 1.2427
R(d) [CG] = 1.0313
R(e) [CT] = 3.6436
R(f) [GT] = 1.0000
gamma shape = 1.7630

ML tree (NNI) for the best AIC model = (((((ON543725_1:0.04621728,


(MZ651026_1:0.00000075,Sp2:0.00373401):0.03004284):0.08169264,
((OM327581_1:1.59509865,OM427490_1:0.05236497):0.02667598,OL679100_1:0.06501618):0.
05226871):0.10671932,OP028904_1:0.47355068):0.17336389,OQ874725_1:0.01474225):0.008
27028,ON922525_1:0.00000013,OQ874719_1:0.00752322);

* AIC MODEL SELECTION : Selection uncertainty

Model -lnL K AIC delta weight cumWeight


------------------------------------------------------------------------
SYM+G 2937.9199 24 5923.8398 0.0000 0.6100 0.6100
K80+G 2942.3674 20 5924.7347 0.8949 0.3899 1.0000
SYM 2948.5967 23 5943.1935 19.3537 3.83e-005 1.0000
K80 2954.1380 19 5946.2760 22.4362 8.19e-006 1.0000
JC+G 2984.9946 19 6007.9892 84.1494 3.25e-019 1.0000
JC 2998.0555 18 6032.1110 108.2712 1.88e-024 1.0000
------------------------------------------------------------------------
-lnL: negative log likelihod
K: number of estimated parameters
AIC: Akaike Information Criterion
delta: AIC difference
weight: AIC weight
cumWeight: cumulative AIC weight

* AIC MODEL SELECTION : Confidence interval

There are 6 models in the 100% confidence interval: [ SYM+G K80+G SYM K80 JC+G JC ]
There was a problem building the html log files: resources/template does not exist.

Program is done.

You might also like