comparison PGAP-1.2.1/PGAP.pl @ 4:70b7a5270968 draft

Uploaded

3:bbb2c473664c

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;

### programs from BLAST
my $formatdb="formatdb";
my $blastall="blastall";

### programs from mcl
my $mcl="mcl";

### programs from mafft
my $mafft="mafft";

### programs from PHYLIP
my $seqboot="seqboot";
my $neighbor="neighbor";
my $consense="consense";
my $dnaml="dnaml";
my $dnadist="dnadist";
my $dnapars="dnapars";

my $count_tree=0;

my $sampleSize=8000; # when calculate the pan-genome size, we will sample $sampleSize combinations
                     # if the total combination number is larger than $sampleSize for specific genomes

4:70b7a5270968

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
use File::Basename;

use lib dirname(__FILE__);

### programs from BLAST
my $formatdb=`which formatdb`;
chomp($formatdb);

my $blastall=`which blastall`;
chomp($blastall);

### programs from mcl
my $mcl=`which mcl`;
chomp($mcl);

### programs from mafft
my $mafft=`which mafft`;
chomp($mafft);

### programs from PHYLIP
my $seqboot=`which seqboot`;chomp($seqboot);
my $neighbor=`which neighbor`;chomp($neighbor);
my $consense=`which consense`;chomp($consense);
my $dnaml=`which dnaml`;chomp($dnaml);
my $dnadist=`which dnadist`;chomp($dnadist);
my $dnapars=`which dnapars`;chomp($dnapars);

my $count_tree=0;

my $sampleSize=8000; # when calculate the pan-genome size, we will sample $sampleSize combinations
                     # if the total combination number is larger than $sampleSize for specific genomes