R: Phylogenetic Methods for Multiple Gene Data

# Phylogenetic Methods for Multiple Gene Data

## Documentation for package ‘apex’ version 1.0.7

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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