[Bioperl-l] distmat matrix
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
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:
> I need to go through a uncorrected distmat matrix (EMBOSS, run
> to filter sequences from an MSA.
> I had a look around and didn't find an obvious candidate. Before I
> 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!
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