You will need a dummy file:

>mel
gtaagttttgagcatttaaatggaagtaaaaggcctactagatgggta--------atttgtgttt-acaaagtg---ccagctagggttaccat-gtcgactttgtgttttttccgcatccact-tagcatcagatgatagcattttt-gcaaatttcaagttttacggcgactgtacgagcgcgttccggtccacagcgcactttttccatacgaccgcagtgcgt---ttgtatgcgtttgtgtgtgtatgtacctgatgtctatcttcctcttctgtgtgtttttg---ttgctttttcgttcggggcgaaagtgctactactg--cggtcgttcggaaaaagtgctgctctcaggca--gacgcctcgccgacagtggccttaaaatttgtattcc--acatagcgtggcaaataattactttttcaacg-tgctcataattgcgatttttgatccatag
>sim
gtatgttttgatcacttaaatt-aagtaaaagacctactagatggcta--------atttgtgatt-acaaagtg---ccagctaggcttaccac-gccgactttgtgttttttccgcatccactctagcatcagatgatagcattttttgcaaatttcaagttttacggcgactgtacgagcgcgttccggtccacagcgcactttt-ccatacgaccgcagtgcgc---gtgcatgcgt--gtgtgtgtatgtacctgatatctctcttcctcttctatgtgattctg---ttgctttttcgttcggggcgaaagtgcgaccactg--cggtcgttc-ggaaaagtgctgctctcaaaca--gacgcctcgccgacagtggccgtaaaatttgtattcc--gcatagcgtggcaaataattactttttcaagg-tgctcataattgtgatttttgatccctag
>yak
gtaagttttgtgctcttatgtt-aagtaaaataccttctagccgggcg--------atttgtgatt-acaaagtg---tcagctatgactaccac-gccgactttgtgtttttttcgcatccgct-tagcgtcagatgatagcattttt-gcaaatttcaagttttacggcgactgtacgagcgcgttccggttaacagcgcacttttcccatacgaccgcagtgcgc---ttgtatgcgt--gtgcttgtatgtacctgatgtctctcttcctcttctttgtgttgttg---ctgccttttcgttcggggcgaaagtgcgaccgctg--cggtcgttcgggaaaagtgatgctctccagca--gacgcctcgccgactgtggccgtaaaatgtgtatttc--gcatagcgtggcatataattacaattccaagg-tactcataatcgcgatttttgatccccag
>pse
gtaagtttt-tgca--taaaat-aactaaaaa---ttgtacgcttt-acagcagatatttatgatttac----cggcccccgcagtgtttttcggagccggaggcaaatttttttcgggtccatt-cggcggcggatgatagca-tttt-gcgaatttctagttatacggcgactgtacgagcgcgtttcg--tcagagctcacttttcagtgacaaccgcagagcggattttggtggtgt--gtgtgtat-----------gcttaagtgtg-cgcgtatgtacctgtatgtctgc-ttt--gttc--ggcgaaagtgt-act-ctgaagggttgttgtcgaaaagtgc-gctctgc-gcatggacgcttcagcgaccgtggcggtaaaattt--attttctgcatagcgtggcaattgctcattttttcgccaat-ctaacccttgatatttctgctctccag

That are the options I have chosen:

$mech->form_number(1);
$mech->set_fields(email => "", -uploaded_file => $upload, -case => "upper", -seqnos => "off", -outorder => "input",);
$mech->tick(-in => "Mlalign_id_pair");
$mech->tick(-in => "Mfast_pair");
$mech->tick(-in => "Mclustalw_aln");
$mech->tick(-output => "fasta_aln");
$mech->tick(-output => "score_html");
$mech->submit();