jmodeltest1

Hpc selection of models of nucleotide substitution

Usage

jmodeltest -d sequenceFileName [-getPhylip] [-ckp checkpointFileName.ckp] [-n executionName] [{-t fixed | BIONJ | ML}] [-u userTreeFileName] [-o outputFileName] [{-S NNI | SPR | BEST}] [-AIC] [-AICc] [-BIC] [-DT] [-c confidenceInterval] [{-s 3 | 5 | 7 | 11 | 203}] [-f] [-i] [-g numberOfCategories] [-uLNL] [-dLRT] [-h confidenceInterval] [-hLRT] [-O ftvwxgp] [-a] [-z] [-p] [-v] [-w] [-tr numberOfThreads] [-machinesfile machinesFileName]

Overview

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model- averaged phylogenetic trees (both topology and branch length), heuristic filtering and automatic logging of user activity.

Options

-a

: estimate model-averaged phylogeny for each active criterion (e.g., -a) (default is false)

-AIC

: calculate the Akaike Information Criterion (e.g., -AIC) (default is false)

-AICc

: calculate the corrected Akaike Information Criterion (e.g., -AICc) (default is false)

-BIC

: calculate the Bayesian Information Criterion (e.g., -BIC) (default is false)

-DT

: calculate the decision theory criterion (e.g., -DT) (default is false)

-c confidenceInterval

: confidence interval (e.g., -c 90) (default is 100)

-ckp checkpointFileName

: Loads a checkpointing file

-d sequenceFileName

: input data file (e.g., -d data.phy)

-dLRT

: do dynamical likelihood ratio tests (e.g., -dLRT)(default is false)

-f

: include models with unequals base frecuencies (e.g., -f) (default is false)

-g numberOfCategories

: include models with rate variation among sites and number of categories (e.g., -g 8) (default is false & 4 categories)

-G threshold

: heuristic search. Requires a threshold > 0 (e.g., -G 0.1)

-getPhylip

: converts the input file into phylip format

-h confidenceInterval

: confidence level for the hLRTs (e.g., -a0.002) (default is 0.01)

-H informationCriterion

: information criterion for clustering search (AIC, AICc, BIC). (default is BIC) this argument applies only for 203 substitution schemes (e.g., -s 203 -H AIC)

-help

: displays this help message

-hLRT

: do hierarchical likelihood ratio tests (default is false) hypothesis testing order can be specified with -O argument

-i

: include models with a proportion invariable sites (e.g., -i) (default is false)

-machinesfile manchinesFileName

: gets the processors per host from a machines file

-n executionName

: execution name for appending to the log filenames (default: current time yyyyMMddhhmmss)

-o outputFileName

: set output file (e.g., -o jmodeltest.out)

-O hypothesisOrder

: hypothesis order for the hLRTs (e.g., -hLRT -O gpftv) (default is ftvwxgp)

: f=freq, t=titvi, v=2ti4tv(subst=3)/2ti(subst>3), w=2tv, x=4tv, g=gamma, p=pinv this argument is used only if -hLRT argument is set 'f','t','v','g','p' are mandatory in any order. 'w' is optional, and 'x' requires 'w' to be present thus, length should be 5, 6 *including 'w') or 7 (including both 'w' and 'x') e.g., -hLRT -O gpfvwxt

-p

: calculate parameter importances (e.g., -p) (default is false)

-r

: backward selection for the hLRT (e.g., -r) (default is forward)

-s numberOfSubstitutionSchemes

: number of substitution schemes (e.g., -s 11) (it has to be 3,5,7,11,203; default is 3)

--set-local-config localConfigurationFile

: set a local configuration file in replacement of conf/jmodeltest.conf

--set-property propertyName=propertyValue

: set a new value for a property contained in the configuration file (conf/jmodeltest.conf)

-S NNI|SPR|BEST

: tree topology search operation option (NNI (fast), SPR (a bit slower), BEST (best of NNI and SPR)) (default is BEST)

-t fixed|BIONJ|ML

: base tree for likelihood calculations (e.g., -t BIONJ)

: fixed (common BIONJ-JC topology)

: BIONJ (Neighbor-Joining topology)

: ML (Maximum Likelihood topology) (default)

-tr numberOfThreads

: number of threads to execute (default is 4)

-u treeFileName

user tree for likelihood calculations: (e.g., -u data.tre)

-uLnL

: calculate delta AIC,AICc,BIC against unconstrained likelihood (e.g., -uLnL)

: (default is false if the input alignment has gaps or ambiguous characters)

-v

: do model averaging and parameter importances (e.g., -v) (default is false)

-w

: write PAUP block (e.g., -w) (default is false)

-z

: strict consensus type for model-averaged phylogeny (e.g., -z) (default is majority rule)

Examples

jmodeltest -d sequenceFileName -i -f -g 4 -BIC -AIC -AICc -DT -v -a -w