Learn R Programming

Rphylip (version 0.1-23)

An R interface for PHYLIP

Description

Rphylip provides an R interface for the PHYLIP package. All users of Rphylip will thus first have to install the PHYLIP phylogeny methods program package (Felsenstein 2013). See http://www.phylip.com for more information about installing PHYLIP.

Copy Link

Version

Install

install.packages('Rphylip')

Monthly Downloads

11

Version

0.1-23

License

GPL (>= 2)

Maintainer

Liam Revell

Last Published

March 26th, 2014

Functions in Rphylip (0.1-23)

Rpenny

R interface for penny
Rtreedist

R interface for treedist
as.proseq

Converts objects to protein sequences, phylip.data, or rest.data object
Rgendist

R interface for gendist
Rcontml

R interface for contml
Rseqboot

R interface for seqboot
Rphylip-package

Rphylip: An R interface for PHYLIP
Rpars

R interface for pars
Rprotpars

R interface for protpars
Rkitsch

R interface for kitsch
Rdnapenny

R interface for dnapenny
Rdnacomp

R interface for dnacomp
Rmix

R interface for mix
Rrestml

R interface for restml
Rconsense

R interface for consense
Rfitch

R interface for fitch
Rclique

R interface for clique
Rneighbor

R interface for neighbor
Rthreshml

R interface for threshml
Rrestdist

R interface for restdist
Rproml

R interfaces for proml and promlk
Rdnaml

R interfaces for dnaml and dnamlk
Rdnadist

R interfaces for dnadist
Rprotdist

R interfaces for protdist
Rcontrast

R interface for contrast
Rdnainvar

R interface for dnainvar
opt.Rdnaml

Parameter optimizer for Rdnaml
primates

Example datasets
setPath

Set path to the folder containing PHYLIP executables for the current R session
Rdollop

R interface for dollop
setupOSX

Help set up PHYLIP in Mac OS X
read.protein

Reads protein sequences from file in multiple formats
Rdnapars

R interface for dnapars
print.proseq

Print method protein sequences, phylip.data, or rest.data object
Rdolpenny

R interface for dolpenny