[Bioperl-l] distmat matrix

Jason Stajich jason.stajich at duke.edu
Wed Feb 15 08:19:41 EST 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  
sequences
Bio::Align::DNAStatistics
and for protein
Bio::Align::ProteinStatistics

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

http://bioperl.org/wiki/Phylogenetics
http://bioperl.org/wiki/HOWTO:Trees
http://bioperl.org/wiki/Module:Bio::Align::DNAStatistics


-jason
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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12




More information about the Bioperl-l mailing list