[BiO BB] Observation: multiple sequence alignment affected by the input sequence order

[Hongyu Zhang]

Dear all,

I've observed that several multiple sequence alignment programs, including ProbCons, ClustalW and Musle, all share the same behavior, i.e., given a group of sequences in FASTA format as the input, if I change the order of the sequences in the input file, the results generated by those programs will change as well. It's not just the sequence order that will change, but also the amino acid matches.

I think it's a little counter-intuitive because one would expect the opposite. Is there a program that can output a stable alignment independent of the input sequence order? Thanks!