use strict;
use warnings;
-use Getopt::Long;
+use Getopt::Long qw(:config auto_version);
use Pod::Usage;
use Carp;
use UNIVERSAL qw(isa);
use Data::Dumper;
use File::Temp;
+use FindBin qw($Bin);
+use lib "$Bin/../lib";
+
use Jpred; # needed to define BLAST environment variables
# my modules
use Run qw(check);
use Paths qw($pairwise $oc $jnet $hmmbuild $hmmconvert $psiblastbin);
-my $VERSION = '3.0.1';
+our $VERSION = '3.0.2';
my $MAX_ALIGN = 1000; # maximum number of alignment sequences allowed
my $NR_CUT = 75; # cut-off seqeunce ID value for defining non-redundancy