my @ctl = glob("/users/sophix/Desktop/prottest3/prottest3/*.aa");

my ($ctltrimmed, $ctlfile, $ctlfiletrimmed);

foreach my $ctlfile (@ctl) {

	if ($ctlfile =~ m/prottest3\/prottest3\/(\S+).aa$/) {$ctlfiletrimmed = $1;}	

	my $out = system("/users/sophix/Desktop/prottest3/prottest3/java.exe -jar prottest-3.0.jar -i " . $ctltrimmed . "-t " . $ctltrimmed . "\.trees" . "-o " . $ctltrimmed . "\.out" . "-all -verbose -all-matrices -threads 3 -G -F -all-distributions -ncat 4");
	
}