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1 : overbeek 1.1 #!/usr/bin/env /Volumes/seagate/FIGdisk/env/mac/bin/perl
2 :    
3 :     BEGIN {
4 :     @INC = qw(
5 :     /Volumes/seagate/FIGdisk/dist/releases/ross/mac/lib
6 :     /Volumes/seagate/FIGdisk/dist/releases/ross/mac/lib/FigKernelPackages
7 :     /Volumes/seagate/FIGdisk/dist/ross/mac/lib
8 :     /Volumes/seagate/FIGdisk/dist/ross/mac/lib/FigKernelPackages
9 :     /Volumes/seagate/FIGdisk/env/mac/lib/perl5/5.8.7/darwin-2level
10 :     /Volumes/seagate/FIGdisk/env/mac/lib/perl5/5.8.7
11 :     /Volumes/seagate/FIGdisk/env/mac/lib/perl5/site_perl/5.8.7/darwin-2level
12 :     /Volumes/seagate/FIGdisk/env/mac/lib/perl5/site_perl/5.8.7
13 :     /Volumes/seagate/FIGdisk/env/mac/lib/perl5/site_perl
14 :     .
15 :     /Volumes/seagate/FIGdisk/config
16 :    
17 :     );
18 :     }
19 :     use Data::Dumper;
20 :     use Carp;
21 :     use FIG_Config;
22 :     $ENV{'BLASTMAT'} = "/Volumes/seagate/FIGdisk/BLASTMAT";
23 :     $ENV{'FIG_HOME'} = "/Volumes/seagate/FIGdisk";
24 :     # end of tool_hdr
25 :     ########################################################################
26 :    
27 :     use FIG;
28 :     use InsertIntoTree;
29 :     use strict;
30 :    
31 :     use gjoseqlib;
32 :     use gjonewicklib;
33 :    
34 :     my $usage = "usage: insert_into_a_tree Alignment Tree [TreeProg] > new.tree\n";
35 :    
36 :     my($aliF,$treeF);
37 :     (
38 :     ($aliF = shift @ARGV) &&
39 :     ($treeF = shift @ARGV)
40 :     )
41 :     || die $usage;
42 :    
43 :     my $tree_prog = (@ARGV > 0) ? $ARGV[0] : undef;
44 :    
45 :     my $ali = &gjoseqlib::read_fasta($aliF);
46 :     my $tree = &gjonewicklib::parse_newick_tree_str(join("",`cat $treeF`));
47 :    
48 :     my $new_tree = &InsertIntoTree::update_old_tree_using_new_ali($ali,$tree,$tree_prog);
49 :     &gjonewicklib::writeNewickTree($new_tree);
50 :    

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