Rphylip: An R interface for PHYLIP

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.

Author
Liam J. Revell, Scott A. Chamberlain
Date of publication
2014-03-26 07:21:03
Maintainer
Liam J. Revell <liam.revell@umb.edu>
License
GPL (>= 2)
Version
0.1-23
URLs

View on CRAN

Man pages

as.proseq
Converts objects to protein sequences, phylip.data, or...
opt.Rdnaml
Parameter optimizer for Rdnaml
primates
Example datasets
print.proseq
Print method protein sequences, phylip.data, or rest.data...
Rclique
R interface for clique
Rconsense
R interface for consense
Rcontml
R interface for contml
Rcontrast
R interface for contrast
Rdnacomp
R interface for dnacomp
Rdnadist
R interfaces for dnadist
Rdnainvar
R interface for dnainvar
Rdnaml
R interfaces for dnaml and dnamlk
Rdnapars
R interface for dnapars
Rdnapenny
R interface for dnapenny
Rdollop
R interface for dollop
Rdolpenny
R interface for dolpenny
read.protein
Reads protein sequences from file in multiple formats
Rfitch
R interface for fitch
Rgendist
R interface for gendist
Rkitsch
R interface for kitsch
Rmix
R interface for mix
Rneighbor
R interface for neighbor
Rpars
R interface for pars
Rpenny
R interface for penny
Rphylip-package
Rphylip: An R interface for PHYLIP
Rproml
R interfaces for proml and promlk
Rprotdist
R interfaces for protdist
Rprotpars
R interface for protpars
Rrestdist
R interface for restdist
Rrestml
R interface for restml
Rseqboot
R interface for seqboot
Rthreshml
R interface for threshml
Rtreedist
R interface for treedist
setPath
Set path to the folder containing PHYLIP executables for the...
setupOSX
Help set up PHYLIP in Mac OS X

Files in this package

Rphylip
Rphylip/inst
Rphylip/inst/CITATION
Rphylip/NAMESPACE
Rphylip/data
Rphylip/data/primates.rda
Rphylip/data/chloroplast.rda
Rphylip/data/restriction.data.rda
Rphylip/data/cotton.rda
Rphylip/data/primates.bin.rda
Rphylip/R
Rphylip/R/Rphylip.R
Rphylip/MD5
Rphylip/DESCRIPTION
Rphylip/man
Rphylip/man/Rpars.Rd
Rphylip/man/Rproml.Rd
Rphylip/man/Rcontml.Rd
Rphylip/man/Rdnainvar.Rd
Rphylip/man/Rdnadist.Rd
Rphylip/man/Rrestdist.Rd
Rphylip/man/Rdnaml.Rd
Rphylip/man/print.proseq.Rd
Rphylip/man/Rclique.Rd
Rphylip/man/Rfitch.Rd
Rphylip/man/setupOSX.Rd
Rphylip/man/Rmix.Rd
Rphylip/man/Rprotdist.Rd
Rphylip/man/Rcontrast.Rd
Rphylip/man/as.proseq.Rd
Rphylip/man/read.protein.Rd
Rphylip/man/Rpenny.Rd
Rphylip/man/setPath.Rd
Rphylip/man/Rprotpars.Rd
Rphylip/man/Rseqboot.Rd
Rphylip/man/Rdnapenny.Rd
Rphylip/man/Rdnapars.Rd
Rphylip/man/primates.Rd
Rphylip/man/Rthreshml.Rd
Rphylip/man/Rgendist.Rd
Rphylip/man/Rconsense.Rd
Rphylip/man/Rdnacomp.Rd
Rphylip/man/Rtreedist.Rd
Rphylip/man/Rkitsch.Rd
Rphylip/man/Rrestml.Rd
Rphylip/man/opt.Rdnaml.Rd
Rphylip/man/Rphylip-package.Rd
Rphylip/man/Rneighbor.Rd
Rphylip/man/Rdolpenny.Rd
Rphylip/man/Rdollop.Rd