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scripts/RNAalisplit.pl  view on Meta::CPAN

}


###############
# subroutines #
###############

sub alisplit {
  my ($alnfile,$odirn) = @_;
  my ($what,$alifold,$rscape);
  my $format = Bio::AlignIO->_guess_format($alnfile);
  print STDERR "Guess input format $format\n";
  my $AlignSplitObject = Bio::RNA::RNAaliSplit->new(ifile => $alnfile,
						    format => $format,
						    odir => $odirn);
  #print Dumper($AlignSplitObject);
  my $dim = $AlignSplitObject->next_aln->num_sequences;
  my $stkfile = $AlignSplitObject->alignment_stk;
  my $dmfile = make_distance_matrix($AlignSplitObject,$method,$odirn);

  # compute Neighbor Joining tree and do split decomposition