[Biopython] Phylogenetic trees with biopython?

[Matthew Strand]

As far as I know (which doesn't say much) Biopython does not wrap the Phylip
programs. However, you can achieve this through some fairly simple
scripting. Phylip allows for options to be specified in command files.

Informally, these command files consists of the same keystrokes you would
enter when running a Phylip program.

A command file to run the program with the default options would look like:
Y\n
This corresponds to pressing Y to accept the default options and pressing
enter for a line break. You can specify any other options here as well. You
can also specify the name of your "infile" (sequence file) on the first line
of the command file.

Then to run phylip with a command file you might execute something like:
phylip protpars < command_file_name

Then to wrap this in Python just programatically generate your command files
and use the os.system command to execute phylip.
(e.g. os.system('phylip kitsch < protpars_commands')

I hope this helps and good luck.

On Mon, Aug 31, 2009 at 10:22 PM, Italo Maia <italo.maia at gmail.com> wrote:

> Is it possible to create phylogenetic trees with biopython alone or i'll
> have to "phylip things up" a little? Phylip doesn't seem to allow execution
> with options, as blast does, per example, and that really botters me. : /
>
> --
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>
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-- 
Matthew Strand
 stran104 at chapman.edu