The bio-linux-phylip package is a wrapper for the standard Debian/Ubuntu package and delivers, through its dependency on the phylip package, the phylip software and documentation. It also provides links to the documentation from the standard location in Bio-Linux systems, and some sampledata for phylip.

The key difference when you install the bio-linux-phylip package is that the phylip programs can be run by just typing their names on the command line. This is the usage expected on many systems, and written into much documentation. So, for example, on Bio-Linux, and many other systems, you would run the dnadist program by typing:

dnadist

on the command line. If you install only the Debian/Ubuntu phylip package, you would need to type:

phylip dnadist

Note: On Bio-Linux, there are two exceptions to the above. These are the phylip programs mix and factor. These program names are common enough to be used by other packages. Thus, to run these on Bio-Linux, you can either type:

mix_phylip
factor_phylip

or, since the Debian/Ubuntu package is also on your system, you can choose to run them by typing:

phylip mix
phylip factor

The programs distributed within the phylip package are:

• clique
• consense
• contml
• contrast
• dnacomp
• dnadist
• dnainvar
• dnaml
• dnamlk
• dnamove
• dnapars
• dnapenny
• dollop
• dolmove
• dolpenny
• drawgram
• drawtree
• factor
• fitch
• gendist
• kitsch
• mix
• move
• neighbor
• pars
• penny
• proml
• promlk
• protdist
• protpars
• restdist
• restml
• retree
• seqboot
• treedist

References:
Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.

Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.