Get pairwise scores from alignment without re-aligning?
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4.3 years ago
mpd • 0

Hi there,

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!

Thanks!

Multiple sequence alignment bit score alignment • 1.3k views
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Why is --distout not useful for your purpose?

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