Hi!
As system takes an array as an argument, I would rewrite your command like this: 
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);

[download]
What exactly would you like to do with your java program?
cpan:://IPC::Run3 works on various operating systems and allows you to process standard output and error messages from your java program separately.
Note: added chdir() after reading comment by saberworks Best wishes

In reply to Re: Calling Java using system() by angiehope
in thread Calling Java using system() by sophix

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