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Bio/SeqFeature/Primer.pm  view on Meta::CPAN

 Usage   : my $tm = $primer->Tm(-salt => 0.05, -oligo => 0.0000001);
 Function: Calculate the Tm (melting temperature) of the primer
 Returns : A scalar containing the Tm.
 Args    : -salt  : set the Na+ concentration on which to base the calculation
                    (default=0.05 molar).
         : -oligo : set the oligo concentration on which to base the
                    calculation (default=0.00000025 molar).
 Notes   : Calculation of Tm as per Allawi et. al Biochemistry 1997
           36:10581-10594. Also see documentation at
           http://www.idtdna.com/Scitools/Scitools.aspx as they use this
           formula and have a couple nice help pages. These Tm values will be
           about are about 0.5-3 degrees off from those of the idtdna web tool.
           I don't know why.

           This was suggested by Barry Moore (thanks!). See the discussion on
           the bioperl-l with the subject "Bio::SeqFeature::Primer Calculating
           the PrimerTM"

=cut

sub Tm {

t/Align/TreeBuild.t  view on Meta::CPAN

# simple topology test - make sure these 2 are sister
is($tree->find_node('YOR262W')->ancestor->id, 
   $tree->find_node('Smik_Contig1103.1')->ancestor->id, 'Make sure two nodes are sister');

# TODO?
# UPGMA tests


# test the bootstrap
my $replicates = &bootstrap_replicates($aln,10);
is(scalar @$replicates, 10,'10 replicates formulated');