[Bioperl-l] Please recommend Perl module to parse phylogentic trees

justin100 bio.justin100 at gmail.com
Fri Mar 4 15:24:51 EST 2011


Hi,

I am writing a script to parse phylogenetic trees. The input will be
trees in Newick format for now (maybe NEXUS in the future).

Quite a few Perl modules can parse phylogenetic trees. For Newick
format, there are Bio::TreeIO and  Bio::Phylo::Parsers. For NEXUS
format, there is Bio::NEXUS. From my understanding, it's not difficult
to convert from Newick to NEXUS or vice versa, if only for the purpose
of parsing trees.

I'd to know the advantages and disadvantages of these modules when
compared with each other. Please recommend one that you think is the
most capable parser (and hopefully has the least bugs).

Thanks.

Justin


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