DNAbin2index            Conversion of DNAbin to Index
EmptyCells              Identify/Delete Spurious Rows and Columns from
                        DNA Alignments
aliscore                Masking of Sequence Alignments with ALISCORE
blastn                  Nucleotide-Nucleotide BLAST
code.simple.gaps        Simple Gap/Indel Coding
collapseUnsupportedEdges
                        Collapse Unsupported Edges/Branches in a
                        Phylogeny
combMyTree              Graft Polytomies on Tips of Phylogeny
del.miss                Delete Missing Data from DNA Sequences
deleteGaps              Remove Gap Positions From DNA Sequences
descendants             Descendants of an Internal Node in a Phylogeny
eoi                     Identification of Stem-Lineage-Edges and MRCAs
fixNodes                Standard Node Numbering in Phylo Objects
forceEqualTipHeights    Equal Tip Heights
gblocks                 Masking of Sequence Alignments with GBLOCKS
index2DNAbin            Conversion of Index to DNAbin
ips-package             Interfaces to Phylogenetic Software
ips.16S                 Bark Beetle 16S Sequences
ips.28S                 Bark Beetle 28S Sequences
ips.cox1                Bark Beetle COX1 Sequences
ips.tree                Ips Phylogeny
mafft                   Sequence Alignment with MAFFT
mafft.merge             Profile Alignment with MAFFT
mrbayes                 Bayesian MCMC Tree Search with MrBayes
mrbayes.lset            Model Settings for MrBayes
mrbayes.mcmc            MCMC Settings for MrBayes
mrbayes.prset           Set Priors for MrBayes
multistate              MULTISTATE
neighboringPairs        Neighboring Nodes in a Minimum Spanning Tree
ntip                    Numbers of Tips of (Sub)trees
partitionfinder         PartitionFinder
pathd8                  PATHd8
phylo2mafft             Convert Trees for MAFFT
phylo2mst               Conversion from PHYLO to MST Object
pis                     Number of Potentially-Informative Sites
prank                   PRANK
raxml                   Maximum Likelihood Tree Estimation with RAxML
raxml.partitions        Partition scheme for RAxML
rbeauti                 XML Input Files for BEAST
rc                      Reverse-Complement of DNA sequences
read                    Reading Sequence Files
read.beast              Read Bayesian Trees
read.beast.table        Extract node data from BEAST chronogram
sister                  Identification of Sister Nodes and Clades
splitIntoClades         Find Monophyletic Subsets in Species Lists
terminalSisters         Find Pairs of Sister Species
tipHeights              Tip Heights in a Phylogenetic Tree
traitRate               Trait-Dependent Shifts in Molecular Rate
trimEnds                Trim Alignment Ends
unlistFirstLevel        Unlist To First Level Only
write.fas               Write DNA Sequences to File
