[Bioperl-l] distmat matrix

Jason Stajich jason.stajich at duke.edu
Wed Feb 15 13:19:41 UTC 2006

Bioperl can parse PHYLIP distance matricies, see Bio::Matrix::IO.  I  
didn't write an EMBOSS distmat result parser but that would be nice  
to have (but check that EMBOSS doesn't already allow output in phylip  
format first).

There is pure-perl distance matrix calculation of a MSA for DNA  
and for protein

There is some initial discussion here on the website, but could  
certainly use some more details.


On Feb 15, 2006, at 5:35 AM, Daniel Lang wrote:

> Hi,
> I need to go through a uncorrected distmat matrix (EMBOSS, run  
> locally)
> to filter sequences from an MSA.
> I had a look around and didn't find an obvious candidate. Before I  
> start
> writing something my own...
> Is there a bioperl parser for reading distmat matrices or can I trick
> the Bio::MapIO parsers for scoring or PHYLIP in doing so?
> If anyone knows of course a tool to generate an uncorrected distance
> matrix of protein MSAs that is supported by bioperl, would be also OK
> for me:)
> I have no experience with the Pise
> (Bio::Tools::Run::PiseApplication::distmat) stuff, but as I understand
> it it's only to execute the application on a remote web server? Or  
> can I
> solve my task with Pise?
> Thanks in advance!
> Daniel
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Jason Stajich
Duke University

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