[Bioperl-l] PHYLIP problem.

#Raul#~~ WeAtHerEd~~ potterbond007 at gmail.com
Thu Jul 17 00:27:30 EDT 2008


I have been trying for 2 days to make the prodist work for my clustalw
PHYLIP output file but even after following the documentation perfectly, the
distance matrix is just not being calculated.

use Bio::Tools::Run::Phylo::Phylip::ProtDist;

my $inputfilename = '/home/rc174/pro/align.phy';
@params = ('MODEL' => 'PAM');
my $prodistfactory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
my ($matrix)= $prodistfactory->run($inputfile);

I am writing the basic code that should work for this program. I am also
attaching my alignment file ( align.phy ). Can you write a program where
this alignment file outputs a phylogenetic tree based on the Kimura model.

Thanks,
Rahul
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