drawing trees

[Catherine Letondal]

Frank Wright wrote:
> Hi Gene,
> 
> >I didn't see any information on the phylip webpage about phylip format
> >and/or conversion tools.  I can do the conversion myself if I can find
> >documentation on the format.

Our Phylip Web server (http://bioweb/seqanal/phylogeny/phylip-uk.html) may help
with format conversion as well as phylogenetic programs chaining.

> 
> PHYLIP FORMAT
> -------------
> 
> PHYLIP format is discussed in the PHYLIP documentation "main" file:
> 
>    http://www.hgmp.mrc.ac.uk/Menu/Help/phylip-main.html
> 
> See section 6.Overview of the input and output formats/ subsection
> 1.Input File Format 
> See the PHYLIP "sequences" documentation for details of how PHYLIP codes
> unknowns and gaps:
> 
>    http://www.hgmp.mrc.ac.uk/Menu/Help/phylip-sequence.html 
> 
> READSEQ
> -------
> The READSEQ program is very useful for converting between alignment
> formats (you may have to edit "." to be "-" though as PHYLIP codes gaps
> differently). 
> 
> ftp://ftp.bio.indiana.edu/molbio/readseq/
> 
> To use:
> 
>   Unix% readseq mygene.msf -format=phylip -output=mygene.phy -a
> 
> There is an old version and a Java version.  I prefer the old one :-).
> 
> 
> Other programs
> --------------
> 
> Jennifer Steinbachs has suggested some programs for reformatting
> alignments.  Here's some additional comments:
> 
> There are other programs that can reformat alignment files.  CLUSTALW
> can be used to read in alignments (option 1) and write them out (option
> 2, suboption 9) without doing an alignment.  I've not used SEQIO but it
> looks useful:
> 
> http://bioweb.pasteur.fr/docs/seqio/seqio.html
> 
> On a PC you could use "export" and "import" facilities in GENEDOC, an
> excellent alignment editor.
> 
> http://www.psc.edu/biomed/genedoc/
> 
> 
> 
> Best Wishes,
> Frank
> --
> Frank Wright
> Biomathematics and Statistics Scotland, 
> SCRI, DUNDEE DD2 5DA, Scotland
> frank at bioss.sari.ac.uk

--
Catherine Letondal -- Pasteur Institute Computing Center