c:\users/sophix/Desktop/prottest3/prottest3>java

##</code><code>##

 -jar prottest-3.0.jar -i alignment1.aa -t tree1.trees  -o output1.out -all -verbose -all-matrices -threads 3 -G -F -all-distributions -ncat 4 
##</code><code>##

my $out = system("/users/sophix/Desktop/prottest3/prottest3/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"); 

##</code><code>##

my $cmd = "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"; 
print $cmd . "\n";
#system( $cmd );