test.submodel.valid.phyml: model validation of the substitution models
In lliu1871/phybase: Basic functions for phylogenetic analysis

test.submodel.valid.phyml

R Documentation

model validation of the substitution models

Description

The function includes chi-squres goodness-of-fit test for validating the substitution model. There are three tests, (1) the chi-square test for base frequencies, (2) the chi-square test for double-nucleotide frequencies, (3) the test for site patterns and the test statistics is sum(|exp_freq-obs_freq|).

Usage

test.submodel.valid.phyml(inputfile, path_phyml, path_seqgen, model, gamma=TRUE, pinv=FALSE, nbootstrap=100)

Arguments

`inputfile`	the sequence file
`path_phyml`	the full path of the phyml binary
`path_seqgen`	the path of the seq-gen binary
`model`	the substitution model
`gamma`	gamma parameter
`pinv`	proportion of invariant sites
`nbootstrap`	The number of bootstrap replicates in the site pattern test.