Phylogenetic Methods for Multiple Gene Data


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Documentation for package ‘apex’ version 1.0.4

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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
apex apex: Extensions of Ape for Multiple Gene 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