You don't necessarily need threads, but you can certainly use them to good effect.

use threads;

## start the first command going
my $t1 = async {
    return qx[ ... ];
};

## Start the second command running.
my $t2 = async {
    return qx[ ... ];
};

## wait for the first to finish and retrieve the output
my $output1 = $t1->join; 

## wait for the second to finish and retrieve the output
my $output2 = $t2->join;
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Doing that in a loop rather than separately is quite trivial.