[Bioperl-l] preparing nexus files for Mr. Bayes

Giovanni Marco Dall'Olio dalloliogm at gmail.com
Wed Jun 11 05:46:37 EDT 2008


Hi,
I was wondering whether there is any bioperl module I can use to
handle nexus files for Mr.Bayes.

mr. Bayes is a program for bayesian estimation of phylogeny, which
uses an alignment file in a customized nexus format as input.
I would need a module to prepare these files, doing tasks like:
- joining more than an alignment in a single file/line
- substitute matching chars with '.'
- customizing parameters displayed in the headers of the output nexus file
- manage mrbayes' extensions, like adding information about partitions and taxas
- adding batch instructions for the mr bayes interpreter
- and similar stuff.

I have tried Bio::AlignIO but I see it doesn't handle all of this,
what I am looing for is bit more specific.
Moreover, I found a bug in the way mrbayes recognizes the output from
Bio::AlignIO (https://sourceforge.net/tracker/index.php?func=detail&aid=1990655&group_id=129302&atid=714418).

Is there any existing module already available?
If there is not, I am going to have to write such scripts anyway.
I would like to contribute them to bioperl, even if I am not a very
good perl programmer, I prefer python.

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