Not being a bio guy, I don't understand your transfer function. However, when I run your code I get several Use of uninitialized value in string. Using Tip #4 from the Basic debugging checklist (Data::Dumper), I see some undef values in your array. Try to eliminate those first. 
use Data::Dumper;
print Dumper(\@arr)

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Arrays in Perl start with index=0 by default, but you start filling the array at index=1. Maybe you want $seqcount++; at the end of your while loop?

If you just want your input file in an array-of-arrays (perldoc perdsc), this is simpler: 

my @arr;
open (B, "temp.dat");
while (my $line=<B>) {
    chomp $line;
    $line =~ s/\s//g;
    my @temp = split //, $line;
    push @arr, [@temp];
}

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In reply to Re: Comparing array of aligned sequences by toolic
in thread Comparing array of aligned sequences by newtoperlprog

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