use strict;
use warnings;

my $align_file=$ARGV[0]; #.py (phylip file right now)

open (F, $align_file) || die "Could not open $align_file: $!";
my @align_matrix; my %HoTaxids;
my @columns;

while (my $line = <F>) {
        chomp($line);
        <F>; # skip firts line of phylip
        next if $line =~ /^\s*$/; # skip blank lines
        my ($taxid,$align_line)=split(/\s/,$line);
        @columns = split(undef, $align_line);#splitting on undef splits each character
        push (@align_matrix, \@columns);
        $HoTaxids{$taxid}=1;
        }
    close(F);

my $num_rows=scalar(keys %HoTaxids);
my $align_len=scalar(@columns);
for (my $i=0;$i<$num_rows;$i++) {
        for (my $j=0;$j<$align_len;$j++){
        if ($align_matrix[$i][$j] ne $align_matrix[$i][$j+1]) {
                print "position\t$j\t is not conserved\n";
        }
}
}