Phylogenetic Methods for Multiple Gene Data

Documentation for package ‘apex’ version 1.0.0

apex-package	apex: Extensions of Ape for Multiple Gene Data
apex	apex: Extensions of Ape for Multiple Gene Data
concatenate	Concatenate genes into a single matrix
dist.multidna	Pairwise distances for multiple gene data
getTree	Build phylogenies from multiple gene data
initialize,multidna-methods	multidna constructor
initialize,multiphyDat-methods	multiphyDat constructor
initialize-method	multidna constructor
initialize-method	multiphyDat constructor
multidna	multidna: class for multiple gene data
multidna-class	multidna: class for multiple gene data
multidna2genind	Convert multidna into genind
multidna2multiphyDat	Convert multidna into genind
multiphyDat	multiphyDat: class for multiple gene data
multiphyDat-class	multiphyDat: class for multiple gene data
multiphyDat2genind	Convert multidna into genind
multiphyDat2multidna	Convert multidna into genind
new.multidna	multidna constructor
new.multiphyDat	multiphyDat constructor
plot-method	Display multidna objects
read.multidna	Read multiple DNA alignments
read.multiFASTA	Read multiple DNA alignments
read.multiphyDat	Read multiple DNA alignments
show-method	Display multidna objects
[-method	Subset multidna objects