Kalign is a fast multiple sequence alignment program for biological
sequences.

Kalign expects the input to be a set of unaligned sequences in fasta
format or aligned sequences in aligned fasta, MSF or clustal format. If
the sequences are already aligned, kalign will remove all gap characters
and re-align the sequences. By default, Kalign automatically detects
whether the input sequences are protein or DNA and selects appropriate
alignment parameters.