[Bioperl-l] distmat matrix

Daniel Lang daniel.lang at biologie.uni-freiburg.de
Wed Feb 15 05:35:40 EST 2006


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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