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Annotation of /FigKernelScripts/make_protein_weights_and_rates.pl

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Revision 1.2 - (view) (download) (as text)

1 : overbeek 1.1
2 :     use proml;
3 :     use gjoseqlib;
4 :     use gjonewicklib;
5 :    
6 :     my $usage = "usage: make_protein_weights_and_rates Alignment Tree > weights.and.rates";
7 :    
8 :     (
9 :     ($ali = shift @ARGV) &&
10 :     ($tree = shift @ARGV)
11 :     )
12 :     || die $usage;
13 :    
14 : golsen 1.2 my @align = &gjoseqlib::read_fasta( $ali );
15 :     my $treeP = &gjonewicklib::read_newick_tree( $tree );
16 : overbeek 1.1
17 : golsen 1.2 my( $cats, $weights ) = proml::estimate_protein_site_rates( \@align, $treeP );
18 :     print scalar @{$cats->[0]}, "\n",
19 :     join( " ", @{$cats->[0]} ), "\n",
20 :     $cats->[1], "\n",
21 :     "$weights\n";

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