[Biopython] Phylogenetic trees with biopython?

[Matthew Strand]

Shoot, I've fudged things up a bit and created a duplicate thread. Here is
my original message, I don't know if someone may be able to delete the other
thread, but hopefully so.

On Mon, Aug 31, 2009 at 11:08 PM, Matthew Strand <stran104 at chapman.edu>wrote:

> 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. : /
>>
>> --
>> "A arrogância é a arma dos fracos."
>>
>> ===========================
>> Italo Moreira Campelo Maia
>> Ciência da Computação - UECE
>> Desenvolvedor WEB e Desktop
>> Programador Java, Python
>> Ubuntu User For Life!
>> -----------------------------------------------------
>> http://www.italomaia.com/
>> http://twitter.com/italomaia/
>> http://eusouolobomal.blogspot.com/
>> ===========================
>>
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>
>
>
> --
> Matthew Strand
>  stran104 at chapman.edu
>



-- 
Matthew Strand
 stran104 at chapman.edu
 phone: (626) 524-4449
 skype: matstrand