Msa Probability
How is the probability calculated from the MSA?
msa
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Which "MSA" are you talking about. Multiple sequence alignment? Mean square average? Metropolitan statistical area? Something else? TLAs (three letter acronyms) need context.
multiple sequence alignment
There are more than a few different algorithms out there for multiple sequence alignment, so you'd be best off just reading the paper describing whichever of these you happen to be using.