aliscore                Masking of Sequence Alignments with ALISCORE
code.simple.gaps        Simple Gap/Indel Coding
collapseUnsupportedEdges
                        Collapse Unsupported Edges
deleteEmptyCells        Delete Spurious Rows and Columns from DNA
                        Alignments
deleteGaps              Remove Gap/Indel Positions from Alignment
descendants             Descendants of an Internal Node in a Phylogeny
fixNodes                Standard Node Numbering in Phylo Objects
gblocks                 Masking of Sequence Alignments with GBLOCKS
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                   DNA Sequence Alignment with MAFFT
mrbayes                 Bayesian MCMC Tree Search with MrBayes
multistate              MULTISTATE
noi                     Identification of MRCAs for Clades
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
read.beast              Read Bayesian Trees
read.beast.table        Extract node data from BEAST chronogram
read.fas                Read DNA Sequences
sister                  Identification of Sister Nodes and Clades
tipHeights              Tip Heights in a Phylogenetic Tree
traitRate               Trait-Dependent Shifts in Molecular Rate
trimEnds                Trim Alignment Ends
write.fas               Write DNA Sequences to File
write.partitioned.nex   Write partitioned and commented NEXUS files
