Then something simple like this might do:

#! perl -slw
use strict;

my $protienFile = shift;

my $size = -S protienFile;
my $chunk = int( $size / 20 );

open IN, '<', $protienFile or die;

my %procs;
for my $n ( 1 .. 20 ) {
    open O, '>', "temp$n.in" or die $!;
    print O, scalar <I> while tell( O ) < ( $n * $chunk );
    close O;
    my $pid;
    if( $pid = fork() ) {
        ++$procs{ $pid };
    }
    elsif( defined $pid ) {
        exec "java -Xmx300m java_code/ALPHAtest -a tables/A.TRAINED -e
+ tables/E.TRAINED -c tables/conf.tat -f temp$n.in > temp$n.out";
    }
    else {
        die "Fork failed";
    }
}

while( keys %procs ) {
    my $pid = wait;
    delete $procs{ $pid };
}

open O, '>', $protienFile . '.out' or die $!;
for my $n ( 1 .. 20 ) {
    open I, '<', "temp$n.out" or die $!;
    print O, <i>;
    close I;
    unlink "temp$n.in", "temp$n.out";
}
close O;
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Note:That's untested.

You might get a little more clever and use the piped-open to run the commands and read the output back directly into the parent for merging, but handling multiple concurrent input streams without mixing up the results gets messy.

If the input data file is really big, it can be worth using named_pipes so you don't have to write copies of the data to the file system.

You'd need a process to seek to the correct point in the file and then write blocks of data to the named pipe, and then the java program can open the named pipe as a regular file and just read from it. The details vary depending which operating system you're on, and it might be too much effort for your particular problem but it can be a useful technique.

IIRC named pipes are a lot easier to work with on Linux/Unix than on Windows, but I haven't used them on Windows for some years - so things might have got better since then.

Oh thanks a lot! I will try it out and see how it works, and, if this is not much to ask, I might bother you again with clarification questions :)