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7.2 years ago
Joe
21k
A friend asked me if there are tools that can output the aforementioned information. A nice simple commandline tool preferably. It occurred to me I don't actually know...
Taking in a MSA, are there any programs that will output a consesus sequence (ideally as a separate fasta file) as well as the per-base or per-Amino sequence identity? So far, my friend has been doing it one at a time in Jalview GUI.
So far from reading posts here and on SeqAnswers, a mashing together of cons and alistats might work. alistats doesn't give %ID per position though.
Is this something that is going to need coding up from scratch? Surely not?
Biopython can give you a quick consensus sequence between multiple sequences, and you can code in a PSM.