ips0.0.12 package

Set Priors for MrBayes

Masking of Sequence Alignments with ALISCORE

XML Parameter Nodes

Nucleotide-Nucleotide BLAST

Simple Gap/Indel Coding

Collapse Unsupported Edges/Branches in a Phylogeny

Graft Polytomies on Tips of Phylogeny

Delete Missing Data from DNA Sequences

Remove Gap Positions From DNA Sequences

Descendants of an Internal Node in a Phylogeny

Conversion of DNAbin to Index

Identify/Delete Spurious Rows and Columns from DNA Alignments

Standard Node Numbering in Phylo Objects

Equal Tip Heights

Masking of Sequence Alignments with GBLOCKS

Conversion of Index to DNAbin

Internal IPS Functions

Interfaces to Phylogenetic Software

Profile Alignment with MAFFT

Sequence Alignment with MAFFT

Model Settings for MrBayes

MCMC Settings for MrBayes

Bayesian MCMC Tree Search with MrBayes

MULTISTATE

Neighboring Nodes in a Minimum Spanning Tree

Numbers of Tips of (Sub)trees

Identification of Stem-Lineage-Edges and MRCAs

PartitionFinder

PATHd8

Convert Trees for MAFFT

Conversion from PHYLO to MST Object

Number of Potentially-Informative Sites

PRANK

Partition scheme for RAxML

Maximum Likelihood Tree Estimation with RAxML

XML Input Files for BEAST

Reverse-Complement of DNA sequences

Read Bayesian Trees

Extract node data from BEAST chronogram

Reading Sequence Files

Identification of Sister Nodes and Clades

Find Monophyletic Subsets in Species Lists

Find Pairs of Sister Species

Tip Heights in a Phylogenetic Tree

Trait-Dependent Shifts in Molecular Rate

Trim Alignment Ends

Unlist To First Level Only

Write DNA Sequences to File