push @args, "-n $options->{ 'mismatches' }";
push @args, "-v $options->{ 'mismatches' }"; # DANGER: using seed mismatches as alignment mismatches - may work, may not!
push @args, "-f" if $type eq "FASTA";
push @args, "-n $options->{ 'mismatches' }";
push @args, "-v $options->{ 'mismatches' }"; # DANGER: using seed mismatches as alignment mismatches - may work, may not!
push @args, "-f" if $type eq "FASTA";