createMLTrees: create maximum likelihood trees from a list of alignments

In JamesStimson/transnp: Transmission inference using SNP data

Description

create maximum likelihood trees from a list of alignments

Usage

createMLTrees(alist, maxit = 10000, optNni = TRUE, bf = basefreqs,
  untangle = TRUE, ...)

Arguments

alist	list of alignments in DNAbin format
maxit	Max number of iterations in optimisation
optNni	(TRUE) optimise the topology of the tree
untangle	flag as to whether to untangle tree, may be needed for small trees
...	further parameters for optim.pml

Value

list of maximum likelihood trees in phylo format

JamesStimson/transnp documentation built on May 30, 2019, 3:51 p.m.