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ips (version 0.0-7)

Interfaces to Phylogenetic Software in R

Description

This package provides functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.

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Version

Install

install.packages('ips')

Monthly Downloads

1,319

Version

0.0-7

License

GPL (>= 2)

Maintainer

Christoph Heibl

Last Published

November 10th, 2014

Functions in ips (0.0-7)

Remove Gap/Indel Positions from Alignment

Read DNA Sequences

Standard Node Numbering in Phylo Objects

Masking of Sequence Alignments with ALISCORE

raxml.partitions

Partition scheme for RAxML

Interfaces to Phylogenetic Software

Descendants of an Internal Node in a Phylogeny

Trim Alignment Ends

Bark Beetle 16S Sequences

XML Input Files for BEAST

Bayesian MCMC Tree Search with MrBayes

Read Bayesian Trees

DNA Sequence Alignment with MAFFT

code.simple.gaps

Simple Gap/Indel Coding

read.beast.table

Extract node data from BEAST chronogram

deleteEmptyCells

Delete Spurious Rows and Columns from DNA Alignments

Number of Potentially-Informative Sites

write.partitioned.nex

Write partitioned and commented NEXUS files

collapseUnsupportedEdges

Collapse Unsupported Edges

Bark Beetle 28S Sequences

Internal IPS Functions

Trait-Dependent Shifts in Molecular Rate

Maximum Likelihood Tree Estimation with RAxML

Identification of MRCAs for Clades

Write DNA Sequences to File

Identification of Sister Nodes and Clades

Masking of Sequence Alignments with GBLOCKS

Tip Heights in a Phylogenetic Tree

Bark Beetle COX1 Sequences