As others already pointed out, there's no reason to use hundreds of files, you can easily concatenate them, either on the fly or afterwards... So use a sequence number, time stamp or whatever you like.

I would like to make a few general observations about your code:

• use the 3-argument form of open
• check the result of open
• use lexical file handles

so, in stead if e.g. open (SEQFILE, ">vik.tmp"), use
open my $seqfile, '>', "vik.tmp" or die "cannot open vik.tmp: $!\n";

• also, check the result of close!

close $seqfile or die "cannot close vik.tmp: $!\n";

• no need to join your line before print

print $seqfile @aln is enough