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| ips-package | Interfaces to Phylogenetic Software |
| aliscore | Masking of Sequence Alignments with ALISCORE |
| code.simple.gaps | Simple Gap/Indel Coding |
| collapseUnsupportedEdges | Collapse Unsupported Edges |
| delete.gaps | Remove Gap/Indel Positions from Alignment |
| 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 |
| fillEndsWithN | Trim Alignment Ends |
| fixNodes | Standard Node Numbering in Phylo Objects |
| gblocks | Masking of Sequence Alignments with GBLOCKS |
| ips | 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 |
| mrbayes.mixed | Bayesian MCMC Tree Search with MrBayes |
| multistate | MULTISTATE |
| multistateMCMC | MULTISTATE |
| multistateML | 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 |
| read.mrbayes | Read Bayesian Trees |
| read.nex | Read DNA Sequences |
| read.phy | Read DNA Sequences |
| read.starbeast | Read Bayesian Trees |
| 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.nex | Write DNA Sequences to File |
| write.partitioned.nex | Write partitioned and commented NEXUS files |
| write.phy | Write DNA Sequences to File |