jmodeltest - HPC selection of models of nucleotide
substitution
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]
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.
-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)
jmodeltest -d sequenceFileName -i -f
-g 4 -BIC -AIC -AICc -DT -v
-a -w
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.