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

Jason Stajich jason.stajich at gmail.com
Sat Mar 19 14:36:49 EDT 2011


Nexus is richer and we only parse the trees from that format. Since the format is a newick tree embedded within it relies on the same code in the newick parser. 

Knowing what you want to do would more likely lead to better answer.  As for bugs - you can search the redmine big tracker to see whether they are reported issues that are unresolved and you can examine the tests in the t directory to see what compliance is tested. 

Jason
Sent from my iPhone-please excuse typos

--
Jason Stajich

On Mar 4, 2011, at 12:24 PM, justin100 <bio.justin100 at gmail.com> wrote:

> 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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