R: Interfaces to Phylogenetic Software in R

# Interfaces to Phylogenetic Software in R

## Documentation for package ‘ips’ version 0.0.13

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

ips-package | Interfaces to Phylogenetic Software
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
deleteEmptyCells | Identify/Delete Spurious Rows and Columns from DNA Alignments
deleteGaps | Remove Gap Positions From DNA Sequences
descendants | Descendants of an Internal Node in a Phylogeny
DNAbin2index | Conversion of DNAbin to Index
EmptyCells | Identify/Delete Spurious Rows and Columns from DNA Alignments
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
identifyEmptyCells | Identify/Delete Spurious Rows and Columns from DNA Alignments
index2DNAbin | Conversion of Index to DNAbin
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 | 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
multistateMCMC | MULTISTATE
multistateML | MULTISTATE
neighboringPairs | Neighboring Nodes in a Minimum Spanning Tree
noi | Identification of Stem-Lineage-Edges and MRCAs
ntip | Numbers of Tips of (Sub)trees
oi | Identification of Stem-Lineage-Edges and MRCAs
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
read.fas | Reading Sequence Files
read.mrbayes | Read Bayesian Trees
read.nex | Reading Sequence Files
read.phy | Reading Sequence Files
read.starbeast | Read Bayesian Trees
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
write.nex | Write DNA Sequences to File
write.phy | Write DNA Sequences to File