---
name: "jmodeltest"
section: "1"
platform: "linux"
package: "jmodeltest"
version: "2.1.10+dfsg-12"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/runjmodeltest-gui"
---

# jmodeltest(1)

HPC selection of models of nucleotide substitution

Part of [runjmodeltest-gui(1)](/runjmodeltest-gui/1.md).

## NAME

jmodeltest - HPC selection of models of nucleotide substitution

## SYNOPSIS

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

## DESCRIPTION

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)

## EXAMPLE

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

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.