I'm looking for a way to extract pairwise bit scores from a multiple sequence alignment without realigning the sequences. Typical scenario is an MSA of around 1000 sequences, produced using MAFFT. I wish to obtain a bit score for each pair of sequences.
Currently I can do this manually by cycling through each sequence and comparing it with each other sequence, but this is slow and I'm sure there must be a quicker way out there, or a method of producing a MSA which outputs the scores. MAFFT --distout is not useful for my purposes.
Any ideas appreciated!