I'm trying to find a fast implementation of a multiple sequence alignment algorithm that I can use from Python. The requirements aren't big. I'll only be aligning a handful (like a dozen) 300bp reads which should be very similar to each other (they come from the same molecule).
But I have to do that about 2 million times, so I'd like to avoid using an external command like in BioPython. I think the overhead of writing a file to disk, creating a process, its disk I/O, and reading the results file might be significant when done for only a dozen reads each time?
tl;dr: Is there something like a ClustalW, MUSCLE, etc package for Python, written in C?