getParams: Get alignment characteristics from a RAxML info file
In fmichonneau/rsowh: rsowh - an R interface for the SO-WH test

Description Usage Arguments Details Value Author(s)

This functions parse the output (info file) of an analysis conducted with RAxML to return the parameters estimated on an alignment as a list.

1	getParams(infoFile)

infoFile

path (including file name) of the info file to be parsed.

Given an ‘info’ file generated by RAxML, this function will return a list that contains all the parameters characterizing the alignement used. This function is specifically (and for now, uniquely) designed to take as an input file, only the RAxML info file generated after invoking the options “-f e -t” while using the models of molecular evolution GTRGAMMA, and GTRGAMMAI.

Trying to use this function on other types of info files generated by RAxML will most likely not work and might give error messages or not.

A list that includes various characteristics about the alignment:

alpha: the shape parameter of the Gamma distribution for the heterogeneity in rates of evolution.
invar: the proportion of invariant sites (empty if the GTRGAMMA model is used)
rateAC, rateAG, rateAT, rateCG, rateGT: transition rates for the GTR model
freqA, freqC, freqG, freqT: relative proportions of the these base pairs in the alignement
nameAlg: the file name of the alignment file
treePath: the file name of the tree with branch lengths optimized given the parameters of the alignment
fileNm: the file name of the info file
seqlen: the sequence length