chdir("c:/users/sophix/Desktop/prottest3/prottest3/");
my @external_command = (
"java", 
"-jar prottest-3.0.jar", 
"-i ".$name."\.aa",  
"-t ".$name."\.trees", 
"-o ".$name."\.out" , 
"-all","-verbose",
"-all-matrices", "-threads 3",
"-G", "-F", "-all-distributions", "-ncat 4");
my $out = system(@external_command);