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Revision 1.8 - (download) (as text) (annotate)
Mon Jan 29 18:59:08 2007 UTC (12 years, 9 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 1.7: +9 -19 lines
debugged version of bring_tree_up_to_ali

use gjoseqlib;
use protdist_neighbor;
use FIG;
use tree_utilities;

$usage = "usage: make_neigh_joining_tree [-a Alpha] Alignment";

my $alpha = undef;
while ($ARGV[0] =~ /^-/)
{
    $_ = shift @ARGV;
    if ($_ =~ s/^-a//) { $alpha = ($_ || shift @ARGV) }
    else               { die "Bad Flag: $_" }
}

(
 ($aliF    = shift @ARGV)
)
    || die $usage;

my %nj_tree_opt = ( tree_format  => 'overbeek' );
$nj_tree_opt{ alpha } = $alpha if $alpha;

my @align   = &gjoseqlib::read_fasta($aliF);
my $nj_tree = protdist_neighbor::protdist_neighbor( \@align, \%nj_tree_opt );
print &tree_utilities::to_newick($nj_tree);

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