ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.
Use the module name modeltest to discover versions available and to load the application.
[]$ modeltest-ng-mpi
MPI Start: Size: 1 Rank: 0
modeltest was compiled without GUI support
Try 'modeltest --help' or 'modeltest --usage' for more information
[]$ modeltest-ng-mpi --help
MPI Start: Size: 1 Rank: 0
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modeltest x.y.z
Copyright (C) 2017 Diego Darriba, David Posada, Alexandros Stamatakis
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Diego Darriba.
--------------------------------------------------------------------------------
Usage: modeltest -i sequenceFilename
[-c n_categories] [-d nt|aa] [-F] [-N]
[-p numberOfThreads] [-q partitionsFile]
[-t mp|fixed|user] [-u treeFile] [-v] [-V]
[-T raxml|phyml|mrbayes|paup]
[--eps optimizationEpsilonValue] [--tol parameterTolerance]
selects the best-fit model of amino acid or nucleotide replacement.
mandatory arguments for long options are also mandatory for short options.
Main arguments:
-d, --datatype data_type_t sets the data type
nt nucleotide
aa amino acid
-i, --input input_msa sets the input alignment file (FASTA or PHYLIP format, required)
-o, --output output_file pipes the output into a file
-p, --processes n_procs sets the number of processors to use (shared memory)
-q, --partitions partitions_file sets a partitioning scheme
-r, --rngseed seed sets the seed for the random number generator
-t, --topology type sets the starting topology
ml maximum likelihood
mp maximum parsimony
fixed-ml-jc fixed maximum likelihood (JC)
fixed-ml-gtr fixed maximum likelihood (GTR)
fixed-mp fixed maximum parsimony (default)
random random generated tree
user fixed user defined (requires -u argument)
-u, --utree tree_file sets a user tree
--force force output overriding
--disable-checkpoint disable checkpoint writing
Candidate models:
-a, --asc-bias algorithm[:values] includes ascertainment bias correction
check modeltest manual for more information
lewis Lewis (2001)
felsenstein Felsenstein
requires number of invariant sites
stamatakis Leaché et al. (2015)
requires invariant sites composition
-f, --frequencies [ef] sets the candidate models frequencies
e: estimated - maximum likelihood (DNA) / empirical (AA)
f: fixed - equal (DNA) / model defined (AA)
-h, --model-het [uigf] sets the candidate models rate heterogeneity
u: *uniform
i: *proportion of invariant sites (+I)
g: *discrite Gamma rate categories (+G)
f: *both +I and +G (+I+G)
r: free rate models (+R)
* included by default
-m, --models list sets the candidate model matrices separated by commas.
use '+' or '-' prefix for updating the default list.
e.g., "-m JTT,LG" evaluates JTT and LG only .
"-m +LG4X,+LG4M,-LG" adds LG4 models and removes LG and from the list.
dna: *JC *HKY *TrN *TPM1 *TPM2 *TPM3
*TIM1 *TIM2 *TIM3 *TVM *GTR
protein: *DAYHOFF *LG *DCMUT *JTT *MTREV *WAG *RTREV *CPREV
*VT *BLOSUM62 *MTMAM *MTART *MTZOA *PMB *HIVB *HIVW
*JTT-DCMUT *FLU *STMTREV LG4M LG4X GTR
* included by default
-s, --schemes [3|5|7|11|203] sets the number of predefined DNA substitution schemes evaluated
3: JC/F81, K80/HKY, SYM/GTR
5: + TrNef/TrN, TPM1/TPM1uf
7: + TIM1ef/TIM1, TVMef/TVM
11: + TPM2/TPM2uf, TPM3/TPM3uf, TIM2ef/TIM2, TIM3ef/TIM3
203: All possible GTR submatrices
-T, --template [tool] sets candidate models according to a specified tool
raxml RAxML (DNA 3 schemes / AA full search)
phyml PhyML (DNA full search / 14 AA matrices)
mrbayes MrBayes (DNA 3 schemes / 8 AA matrices)
paup PAUP* (DNA full search / AA full search)
Other options:
--eps epsilon_value sets the model optimization epsilon
--tol tolerance_value sets the parameter optimization tolerance
--smooth-frequencies forces frequencies smoothing
-g, --gamma-rates [a|g] sets gamma rates mode
a uses the average (or mean) per category (default)
m uses the median per category
--disable-checkpoint does not create checkpoint files
-H, --no-compress disables pattern compression
modeltest ignores if there are missing states
-k, --keep-params keep branch lengths fixed
-v, --verbose run in verbose mode
--help display this help message and exit
--version output version information and exit
Exit status:
0 if OK,
1 if minor problems (e.g., invalid arguments or data),
2 if serious trouble (e.g., execution crashed).
Report modeltest bugs to diego.darriba@h-its.org
ModelTest home page: <http://www.github.com/ddarriba/modeltest/>
[]$ modeltest-ng-mpi --usage
MPI Start: Size: 1 Rank: 0
_ _ _ _ _ _ _____
| | | | | | | | \ | |/ ____|
_ __ ___ ___ __| | ___| | |_ ___ ___| |_ | \| | | __
| '_ ` _ \ / _ \ / _` |/ _ \ | __/ _ \/ __| __| | . ` | | |_ |
| | | | | | (_) | (_| | __/ | || __/\__ \ |_ | |\ | |__| |
|_| |_| |_|\___/ \__,_|\___|_|\__\___||___/\__| |_| \_|\_____|
--------------------------------------------------------------------------------
modeltest x.y.z
Copyright (C) 2017 Diego Darriba, David Posada, Alexandros Stamatakis
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Diego Darriba.
--------------------------------------------------------------------------------
Usage: modeltest -i sequenceFilename
[-c n_categories] [-d nt|aa] [-F] [-N]
[-p numberOfThreads] [-q partitionsFile]
[-t mp|fixed|user] [-u treeFile] [-v] [-V]
[-T raxml|phyml|mrbayes|paup]
[--eps optimizationEpsilonValue] [--tol parameterTolerance] |
This is just an example, please modify appropriately with the account name, etc
#!/bin/bash #SBATCH --job-name=modeltest #SBATCH --nodes=1 #SBATCH --cpus-per-task=8 #SBATCH --partition=teton #SBATCH --account=arcc #SBATCH --time=1-00:00:00 echo "SLURM_JOB_ID:" $SLURM_JOB_ID echo "SLURM_JOB_NAME:" $SLURM_JOB_NAME echo "SLURM_JOB_PARTITION" $SLURM_JOB_PARTITION echo "SLURM_JOB_NUM_NODES:" $SLURM_JOB_NUM_NODES echo "SLURM_JOB_NODELIST: " $SLURM_JOB_NODELIST echo "SLURM_TASKS_PER_NODE:" $SLURM_TASKS_PER_NODE echo "SLURM_CPUS_ON_NODE:" $SLURM_CPUS_ON_NODE echo "SLURM_CPUS_PER_TASK:" $SLURM_CPUS_PER_TASK module load modeltest/0.1.6 modeltest-ng-mpi -i example-data/dna/channa.fas -p $SLURM_CPUS_PER_TASK |