If your code is correct, you could reduce it by trying this (untested): 
sub load_seqs{
    local $ARGV = qw /q1.fa q2.fa/;
    while(my $line = <>){
        if($line =~ m/^(?!\>).*\n$/){push (@{$_[0]},$line)};
    }
}

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In reply to Re: use of diamond operator for multiple files by Laurent_R
in thread use of diamond operator for multiple files by aeqr

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