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Revision 1.5 - (download) (as text) (annotate)
Mon Jan 8 19:47:28 2007 UTC (12 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.4: +8 -6 lines
add tree_neighbors and latest phylogeny stuff

########################################################################


use FIG;
use InsertIntoTree;
use strict;

use gjoseqlib;
use gjonewicklib;

my $usage = "usage: insert_into_a_tree [-c CheckPointFile] [-a Alpha] Alignment Tree [TreeProg] > new.tree\n";

my $check_point = undef;
my $alpha       = undef;
while ($ARGV[0] =~ /^-/)
{
    $_ = shift @ARGV;
    if ($_ =~ s/^-a//)    { $alpha = ($_ || shift @ARGV) }
    elsif ($_ =~ s/^-c//) { $check_point = ($_ || shift @ARGV) }
    else                  { die "Error: invalid flag $_\n$usage" }
}

my($aliF,$treeF);
(
 ($aliF  = shift @ARGV) &&
 ($treeF = shift @ARGV)
)
    || die $usage;

my $tree_prog = (@ARGV > 0) ? $ARGV[0] : undef;

my $ali  = &gjoseqlib::read_fasta($aliF);
my $tree = &gjonewicklib::parse_newick_tree_str(join("",`cat $treeF`));

my ($new_tree,$lnlik) = &InsertIntoTree::update_old_tree_using_new_ali( align => $ali,
									tree => $tree,
									tree_prog => $tree_prog,
									check_point => $check_point,
									alpha => $alpha
								      );
print "Ln Likelihood = $lnlik\n//\n";
&gjonewicklib::writeNewickTree($new_tree);
print "///\n";


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