drawing trees

[Frank Wright]

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.

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