ModelTest

Overview

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.

Using

Use the module name modeltest to discover versions available and to load the application.

Example

[]$ 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 _ _ _ _ _ _ _____ | | | | | | | | \ | |/ ____| _ __ ___ ___ __| | ___| | |_ ___ ___| |_ | \| | | __ | '_ ` _ \ / _ \ / _` |/ _ \ | __/ _ \/ __| __| | . ` | | |_ | | | | | | | (_) | (_| | __/ | || __/\__ \ |_ | |\ | |__| | |_| |_| |_|\___/ \__,_|\___|_|\__\___||___/\__| |_| \_|\_____| -------------------------------------------------------------------------------- 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]

Batch Example

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