Hi all, I have an alignment file and I want to analyze it and output all of the positions that are not conserved. I was thinking of reading in the file as an array of arrays. Below is an example input file. And below that is my current code. Which currently produces the wrong output, and I feel is probably not the most correct way to go about this. Any help is appreciated. 

5 15
1 ATCG--ATCG-ATCG
2 ATGC--ATCG-ATCG
3 ATGC-A-TCG-ATCG
4 ATGC--ATCG-ATCG
5 ATCG--ATCG-AACG

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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 split
+s 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";
        }
}
}

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In reply to manipulating alignment data by AWallBuilder

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