RMPD                    Ratio of mean phylogenetic distance of two
                        phylogenetic trees
add.mat                 Add matrix to current matrix
aln2dat                 Convert ClustalX alignment data to dataframe
appendchar              Paste character according to the longest
                        character.
complement              Get the complement sequences
dat2phy                 Convert dataframe to phylip format
del.tree.tip            Randomly Delete tree tip labels
dimension               Get the dimension of the matrix defined by
                        "XnYm" labels
edgesub                 Substitute character for a sequence from both
                        sides.
fasta.split             Split the fasta object to fasta objects
fmatch                  Find the matching index
formatXY                Formating XY label
framsub                 Pattern of substitutions of a dataframe.
gini                    Gini coefficient of inequality
hcreorder               Reorder the height for hclust object
imagevect               Image plot of a numeric vector
inequality              The inequality of a cutting time
meangini                Mean Gini coefficient
phy2dat                 Convert phylip file to dataframe
phylocom.comdist        Calculating phylogenetic comdist using Phylocom
phylocom.comstruct      Calculating community phylogenetic structure
                        using Phylocom
phylocom.pd             Calculate phylogenetic diversity using Phylocom
phylocom.phylosor       Calculating Phylosor similarity
phyloshuffle            Tip label shuffling of a phylogenetic tree
phylotools-package      Phylogenetic tools for ecologists
plotcut                 Cutting the phylogenetic cutting pattern by a
                        given time or times
plotscale               Rescaling the individuals occurred in a
                        Forestry Dynamic Plot
read.phylip             Read phylip file to memory.
rename.fasta            Renaming a fasta object given a reference table
resid.tree              The undeleted terminals of a phylogenetic tree
reverse                 Get the reverse sequence.
rh                      Generating random time between the oldest node
                        and the latest node
rm.col                  Delete specified columns for dataframe or
                        matrix
seq2fasta               Convert Seq file to fasta format
sub.tip.label           Substitute the tip labels of a phylogenetic
                        tree
supermat                Build super matrix using PHYLIP files
uniquefasta             Deleting duplicated sequences in fasta object
write.mat               Save supermatrix
