drawing trees

[Jennifer Steinbachs]

I like to use Seaview to make the conversion (I don't have the website
handy but a google search should produce it quickly).  ClustalX (and maybe
clustalw) also produce Phylip files.  I thought the Phylip website had
information on the format, but it's been a while since I've actually
perused the documentation.  The phylip docs should definitely have
complete information.

If I recall correctly, it is something like:

#sequences #nucleotide_sites
sequence_name sequence
sequence_name sequence

etc.

There used to be a 10 character limit on sequence_name, but I don't know
if that holds with the latest version - I use PAUP* mostly for my
analyses.  Sequence can be non-interleaved or interleaved.

-jennifer

On Mon, 27 Aug 2001, Gene Cutler wrote:

 >Thanks Jennifer.  One more question:
 >
 >>Put your aligned sequences into PHYLIP format
 >
 >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.
 >
 >>If you aren't certain of the differences between the different
 >>tree-building algorithms, you should get your hands on Nei and Kumar 2000
 >>Molecular Evolution and Phylogenetics ISBN 0-19-513585-7.  The other good
 >>reference for phylogenetics is Hillis et al 1996 Molecular Systematics
 >>ISBN 0-87893-282-8 Chapter 11.
 >
 >That's useful too.  Thanks again.
 >
 >
 >

-- 
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J. Steinbachs, Ph.D.
Computational Biologist
http://compbiology.org
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