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.