An R interface for PHYLIP

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Documentation for package ‘Rphylip’ version 0.1-23

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Rphylip-package Rphylip: An R interface for PHYLIP
as.phylip.data Converts objects to protein sequences, phylip.data, or rest.data object
as.proseq Converts objects to protein sequences, phylip.data, or rest.data object
as.rest.data Converts objects to protein sequences, phylip.data, or rest.data object
chloroplast Example datasets
clearPath Set path to the folder containing PHYLIP executables for the current R session
cotton Example datasets
opt.Rdnaml Parameter optimizer for Rdnaml
primates Example datasets
primates.bin Example datasets
print.phylip.data Print method protein sequences, phylip.data, or rest.data object
print.proseq Print method protein sequences, phylip.data, or rest.data object
print.rest.data Print method protein sequences, phylip.data, or rest.data object
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
Rdnamlk 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
restriction.data Example datasets
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 Rphylip: An R interface for PHYLIP
Rproml R interfaces for proml and promlk
Rpromlk 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 current R session
setupOSX Help set up PHYLIP in Mac OS X