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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 13);
for my $mod ( qw(Bio::Align::DNAStatistics
Bio::Align::ProteinStatistics
Bio::Align::Utilities
Bio::AlignIO
Bio::Tree::DistanceFactory
Bio::TreeIO) ) {
use_ok($mod);
}
}
my $debug = test_debug();
use Bio::Align::Utilities qw(:all);
my $in = Bio::AlignIO->new(-format => 'clustalw',
-file => test_input_file('pep-266.aln'));
my $aln = $in->next_aln();
isa_ok($aln, 'Bio::SimpleAlign','SimpleAlign object parsed out');
my $pstats = Bio::Align::ProteinStatistics->new(-verbose => $debug);
my $matrix = $pstats->distance(-method => 'Kimura',
-align => $aln);
isa_ok($matrix,'Bio::Matrix::MatrixI','Protein distance matrix retrieved');
my $treebuilder = Bio::Tree::DistanceFactory->new(-method => 'NJ');
my $tree = $treebuilder->make_tree($matrix);
isa_ok($tree,'Bio::Tree::TreeI', 'Tree object gotten back');
my ($cn) = $tree->find_node('183.m01790');
# brlens checked against tree generated by PHYLIP NJ
is($tree->find_node('AN2438.1')->branch_length, '0.28221','NJ calculated Branch length');
is($tree->find_node('FG05298.1')->branch_length, '0.20593','NJ calculated Branch length');
# simple topology test - make sure these 2 are sister
is($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');
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