[Bioperl-l] Phylip format for phylogeny

[Richard Copley]

> In the "there must be a way to do this" department, I am working on a phylogeny project, and I would like to take clustalw output, find the common aligned region (i.e., the region without gaps) write it out in phylip format and use it in one or more of the available phylogeny tools. Converting clustalw to phylip format is trivial, but is there a way to find and extract a region from all of the sequences in an alignment? (I can't find it in the documentation.)

Jose Castresana's Gblocks program is a useful way to extract well 
aligned blocks for phylogenetic analysis.

http://monstre1.imim.es/~castresa/Gblocks/Gblocks.html


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Richard Copley      | Wellcome Trust Centre for Human Genetics
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