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
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
as.proseq               Converts objects to protein sequences,
                        phylip.data, or rest.data object
opt.Rdnaml              Parameter optimizer for Rdnaml
primates                Example datasets
print.proseq            Print method protein sequences, phylip.data, or
                        rest.data object
read.protein            Reads protein sequences from file in multiple
                        formats
setPath                 Set path to the folder containing PHYLIP
                        executables for the current R session
setupOSX                Help set up PHYLIP in Mac OS X
