JMODELTEST(1)

💖 NAME 💖

jmodeltest — bestie, this is your HPC-powered glow-up for picking 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 🌸

okay so jModelTest is literally the tool you use to do statistical selection of best-fit models of nucleotide substitution. it's giving "which model ate and which one flopped" energy 🫶

it implements five different model selection strategies:

• hierarchical likelihood ratio tests (hLRT)
• dynamical likelihood ratio tests (dLRT)
• Akaike information criterion (AIC)
• Bayesian information criterion (BIC)
• a decision theory method (DT)

it also hands you estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. iconic 👑

jModelTest 2 brings High Performance Computing (HPC) capabilities to the party, plus extra features like new strategies for tree optimization, model-averaged phylogenetic trees (both topology and branch length), heuristic filtering and automatic logging of user activity. no cap 🔥

💅 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.

k that's the whole thing bestie 💖 this page is from jmodeltest 2.1.10 and it's dated August 2016. go pick some models, you got this 🦋✨