Thanks for your input - very useful. I skipped the BioPerl modules as I wanted the script to be passed around non-BioPerl users. After further help and modification the final product was. 
use strict;
use warnings;

my $in = $ARGV[0];

my $frequencies;
my $maxCol = 0;


open (IN, "$in") or die "cannot open $in!\n";

while (my $line = <IN>) {
    chomp $line;

    my ($name, $seq) = split ("\t", $line);
    if (defined $seq) {    
    my @bases = split '', $seq;
    $maxCol=@bases; 
    for (my $i=0; $i<@bases; $i++) {
        ++$frequencies->{$bases[$i]}[$i];
#        if ($maxCol < @bases) {
#        $maxCol = @bases;
#        }
    }
    }
}


print_hoa($frequencies, $maxCol);


#foreach my $base (keys %frequencies) {
#    $frequencies{$base}[$_] ||= 0 for 0 .. $maxCol;
#    print "$base @{$frequencies{$base}}\n";
#}

##Subroutine that prints a hash fo arrays reference.
sub print_hoa {
    my ($hashref, $len) = @_;

    for my $person (sort keys %{$hashref}) {
    my $array = $hashref->{$person};
    my @array_print = @$array;
    print "$person\t";

    foreach my $num (@array_print) {
        if (defined $num) {
        print "$num ";
        } else {
        print "0 ";
        }
    }
    my $i =@array_print;
    if ($i<$len) {
        my $z_pr = $len-$i;
        print "0 " x $z_pr, "\n";
    } else {
        print "\n";
    }
    }
}

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In reply to Re^2: To count letters (%identity) in DNA alignment by sedm1000
in thread To count letters (%identity) in DNA alignment by sedm1000

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