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Annotation of /FigKernelScripts/make_neigh_joining_tree.pl

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1 : overbeek 1.8 use gjoseqlib;
2 :     use protdist_neighbor;
3 : overbeek 1.1 use FIG;
4 :     use tree_utilities;
5 :    
6 : overbeek 1.8 $usage = "usage: make_neigh_joining_tree [-a Alpha] Alignment";
7 : overbeek 1.1
8 : overbeek 1.2 my $alpha = undef;
9 :     while ($ARGV[0] =~ /^-/)
10 :     {
11 :     $_ = shift @ARGV;
12 :     if ($_ =~ s/^-a//) { $alpha = ($_ || shift @ARGV) }
13 :     else { die "Bad Flag: $_" }
14 :     }
15 :    
16 : overbeek 1.1 (
17 : overbeek 1.8 ($aliF = shift @ARGV)
18 : overbeek 1.1 )
19 :     || die $usage;
20 :    
21 : overbeek 1.8 my %nj_tree_opt = ( tree_format => 'overbeek' );
22 :     $nj_tree_opt{ alpha } = $alpha if $alpha;
23 : overbeek 1.2
24 : overbeek 1.8 my @align = &gjoseqlib::read_fasta($aliF);
25 :     my $nj_tree = protdist_neighbor::protdist_neighbor( \@align, \%nj_tree_opt );
26 :     print &tree_utilities::to_newick($nj_tree);

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