Can you please suggest web applications or packages for R/Python, that don't use PSI-Blast and make PSSM directly from an alignment file? Thanks in advance.
Here's a possible solution in python. As far as I know, there aren't any good packages for this purpose in R.
Haven't tried the service below because I don't know why anyone would use something other than PSI-BLAST for this task, but here goes:
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