drawing trees

[David Martin]

Remember that in the Phylip programs distributed as an EMBASSY package,
EMBOSS will do the sequence conversions for you.

The programs to run are the same name with an e prepended. It also has the
various options in ACD format so the programs can be fully scripted. The
two programs that haven't been EMBOSSised are DRAWTREE and DRAWGRAM.

..d

On Mon, 27 Aug 2001, Jennifer Steinbachs wrote:

>
> 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.
>  >
>  >
>  >
>
>

----------------------------------
David Martin PhD
Bioinformatics Scientific Officer
Wellcome Trust Biocentre, Dundee
----------------------------------