my $fasta = $ARGV[0];
my $seqio = Bio::SeqIO->new(-file => $fasta);
while(my $seqobj = $seqio->next_seq) {
	my $id  = $seqobj->display_id;
	my $seq = $seqobj->seq;
	$sequences{$id} = $seq;
}
open my $IN2, '<', $ARGV[1] or die "$!";
while (<$IN2>) {
	# Subsample the FASTA sequences
}