Phylogenetic Methods for Multiple Gene Data

---

Documentation for package ‘apex’ version 1.0.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

accessors	multidna Accessors
add.gaps	Add gap-only sequences for missing data
add.gaps-method	Add gap-only sequences for missing data
add.gaps.generic	Add gap-only sequences for missing data
add.gaps.multidna	Add gap-only sequences for missing data
add.gaps.multiphyDat	Add gap-only sequences for missing data
concatenate	Concatenate genes into a single matrix
concatenate-method	Concatenate genes into a single matrix
concatenate.generic	Concatenate genes into a single matrix
concatenate.multidna	Concatenate genes into a single matrix
concatenate.multiphyDat	Concatenate genes into a single matrix
data.frameOrNULL	multidna: class for multiple gene data
dist.multidna	Pairwise distances for multiple gene data
getLocusNames	multidna Accessors
getLocusNames,multidna	multidna Accessors
getLocusNames,multiphyDat	multidna Accessors
getLocusNames-method	multidna Accessors
getNumInd	multidna Accessors
getNumInd,multidna	multidna Accessors
getNumInd,multiphyDat	multidna Accessors
getNumInd-method	multidna Accessors
getNumLoci	multidna Accessors
getNumLoci,multidna	multidna Accessors
getNumLoci,multiphyDat	multidna Accessors
getNumLoci-method	multidna Accessors
getNumSequences	multidna Accessors
getNumSequences,multidna	multidna Accessors
getNumSequences,multiphyDat	multidna Accessors
getNumSequences-method	multidna Accessors
getSequenceNames	multidna Accessors
getSequenceNames,multidna	multidna Accessors
getSequenceNames,multiphyDat	multidna Accessors
getSequenceNames-method	multidna Accessors
getSequences	multidna Accessors
getSequences,multidna	multidna Accessors
getSequences,multiphyDat	multidna Accessors
getSequences-method	multidna Accessors
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
listOrNULL	multidna: class for multiple gene data
multidna	multidna: class for multiple gene data
multidna-class	multidna: class for multiple gene data
multidna2alignment	Convert from multidna into alignment (seqinr)
multidna2genind	Convert multidna into genind
multidna2multiphyDat	Conversions between multidna and multiphyDat
multiphyDat	multiphyDat: class for multiple gene data
multiphyDat-class	multiphyDat: class for multiple gene data
multiphyDat2alignment	Convert from multidna into alignment (seqinr)
multiphyDat2genind	Convert multidna into genind
multiphyDat2multidna	Conversions between multidna and multiphyDat
new.multidna	multidna constructor
new.multiphyDat	multiphyDat constructor
plot-method	Display multidna objects
plot.multidna	Display multidna objects
read.multidna	Read multiple DNA alignments
read.multiFASTA	Read multiple DNA alignments
read.multiphyDat	Read multiple DNA alignments
rm.gaps	Remove gap-only sequences for missing data
rm.gaps-method	Remove gap-only sequences for missing data
rm.gaps.generic	Remove gap-only sequences for missing data
rm.gaps.multidna	Remove gap-only sequences for missing data
rm.gaps.multiphyDat	Remove gap-only sequences for missing data
setLocusNames<-	multidna Accessors
setLocusNames<-,multidna	multidna Accessors
setLocusNames<-,multiphyDat	multidna Accessors
setLocusNames<--method	multidna Accessors
show-method	Display multidna objects
show-method	Display multiphyDat objects
show.multidna	Display multidna objects
show.multiphyDat	Display multiphyDat objects
[-method	Subset multidna objects
[.multidna	Subset multidna objects
[.multiphyDat	Subset multidna objects