arnold%gandal.dnet@ASMUS1.GENETICS.UGA.EDU (11/22/90)
There are four things that come to mind that PHYLIP needs:
1) point and click interface. I think PHYLIP has the widest
range of methods, but it is more difficult to use than PAUP.
X-windows (and hence DECwindows may be a possible standard)
2) analysis using extensions of the Lake invariants for more
than 5 taxa.
3) more graphics
4) conversion routines for output from GCG to PHYLIP data format, i.e
TOPHYLIP and TOGCG.
I hope you mean the bulletin board as a posting, Joe. I am a newcomer,
rather than EMAIL to you.
ARNOLD%GANDAL.DNET@ASMUS1.GENETICS.UGA.EDUgilbertd@ogre.cica.indiana.edu (Don Gilbert) (11/23/90)
In article <9011221446.AA05075@asmus1.genetics.uga.edu> arnold%gandal.dnet@ASMUS1.GENETICS.UGA.EDU writes: >4) conversion routines for output from GCG to PHYLIP data format, i.e >TOPHYLIP and TOGCG. You can use ReadSeq now to convert from GCG to Phylip format (it doesn't yet do the reverse). Obtain it via anonymous ftp to iubio.bio.indiana.edu, cd [archive.molbio.readseq], mget *.c and mget *.h and mget *.doc to get the C source and documents, or binary get readseq.arc to get an archive file that includes a VMS shell. I would much prefer to see Phylip read (and if needed, write) sequence data using the IntelliGenetics format. This format is widely used now, and some multiple aligners already produce this output. The current Phylip 3.3 sequence input format, with its interleaving of species, is a pain to translate to/from. While many multi-aligners produce some sort of interleaved output for _display_, all of these require extensive hand editting to fit into Phylip format. I am working with output from another program now that uses an interleaved format: about 150 species with 2000+ bases each. Normally programs read 1 sequence at a time. This means 150 passes thru a 600 kilobyte file ... it takes a while. A format with one sequence after another can be read in one gulp. -- Don