Kalign is a fast multiple sequence alignment program for biological sequences.
Align sequences and output the alignment in MSF format:
kalign -i BB11001.tfa -f msf -o out.msf
Align sequences and output the alignment in clustal format:
kalign -i BB11001.tfa -f clu -o out.clu
Re-align sequences in an existing alignment:
kalign -i BB11001.msf -o out.afa
Reformat existing alignment:
kalign -i BB11001.msf -r afa -o out.afa