[Bioperl-l] parser for dnadist from the phylip package

Jason Stajich jason at cgt.duhs.duke.edu
Tue Jun 29 15:12:20 EDT 2004

I guess no one has written this wrapper yet.  Still looking for
volunteers to help.  It has basically been Shawn Hoon and myself writing
the PHYLIP wrappers and we've only done the ones we needed.

In the latest (CVS HEAD) bioperl you can also just do
my $stats = Bio::Align::DNAStatistics->new;
my $matrix = $stats->distance(-align => $aln, -method => "Jukes-Cantor");

These are the ones currently implemeted:
 JukesCantor [jc|jukes|jukescantor|jukes-cantor]
 Uncorrected [jcuncor|uncorrected]
 Kimura [k2|k2p|k80|kimura]
 Tamura [t92|tamura|tamura92]
 TajimaNei [tajimanei|tajima\-nei]

On Tue, 29 Jun 2004, martin wrote:

> Hi,
> I'm looking to run dnadist on a series of multiple sequence alignments
> (held as Bio::Align objects).  For protein alignments, the process seems
> to be catered for (from what I can tell from the documentation) by
> Bio::Tools::Phylo::Phylip::ProtDist
> and
> Bio::Tools::Run::Phylo::Phylip::ProtDist.
> Does anyone know if there's an analogous object for dnadist, or whether
> the ProtDist modules could be coerced into working?
> Any pointers appreciated.

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

More information about the Bioperl-l mailing list