/usr/bin/bp_nexus2nh is in bioperl 1.7.1-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | #!/usr/bin/perl
=head1 NAME
bp_nexus2nh - convert nexus format trees (from PAUP* and MrBayes) to new hampshire
=head1 SYNOPSIS
bp_nexus2nh file.nexus > file.nh
# OR pipe in through STDIN
cat file.nexus | bp_nexus2nh > file.nh
# OR specify an output
bp_nexus2nh -o file.nh file.nexus
=head1 DESCRIPTION
Convert Nexus Tree files into Newick/New Hampshire format tree files.
=cut
use strict;
use warnings;
use Bio::TreeIO;
use Getopt::Long;
my $outfile;
GetOptions('o|out|outfile:s' => \$outfile);
my $in = Bio::TreeIO->new(-format => 'nexus', -fh => \*ARGV);
my $out;
if( $outfile ) {
$out= Bio::TreeIO->new(-format => 'newick',
-file => ">$outfile");
} else {
# write to STDOUT
$out= Bio::TreeIO->new(-format => 'newick');
}
while( my $t = $in->next_tree ) {
$out->write_tree($t);
}
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