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revision 1.4, Sat Jan 6 17:39:41 2007 UTC revision 1.5, Mon Jan 8 19:47:28 2007 UTC
# Line 32  Line 32 
32  my $ali  = &gjoseqlib::read_fasta($aliF);  my $ali  = &gjoseqlib::read_fasta($aliF);
33  my $tree = &gjonewicklib::parse_newick_tree_str(join("",`cat $treeF`));  my $tree = &gjonewicklib::parse_newick_tree_str(join("",`cat $treeF`));
34    
35  my $new_tree = &InsertIntoTree::update_old_tree_using_new_ali( align => $ali,  my ($new_tree,$lnlik) = &InsertIntoTree::update_old_tree_using_new_ali( align => $ali,
36                                                                 tree => $tree,                                                                 tree => $tree,
37                                                                 tree_prog => $tree_prog,                                                                 tree_prog => $tree_prog,
38                                                                 check_point => $check_point,                                                                 check_point => $check_point,
39                                                                 alpha => $alpha                                                                 alpha => $alpha
40                                                               );                                                               );
41    print "Ln Likelihood = $lnlik\n//\n";
42  &gjonewicklib::writeNewickTree($new_tree);  &gjonewicklib::writeNewickTree($new_tree);
43    print "///\n";
44    

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