in Clustal-Omega you can specify the output format for the alignment with the option --outfmt:
--outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fasta)
I would like to have more than one of these output files. do you know if you can do it in one go? it would be quite unfortunate to have to run the program many times just to have a different output.