GPU-accelerated multiple sequence alignment tools

Question

[jet]

The other day I was trying to do my own multiple sequence alignment files using Clustal Omega. For around 70k protein sequences, it took more than 15 hours (not sure about the exact time), and I was wondering if this was normally the case.

I was also wondering if there are any tools that utilize GPUs for multiple sequence alignments. Because from what I know Clustal Omega does not have GPU acceleration.

[Michael]

For around 70k protein sequences, it took more than 15 hours

Without any exact measure on my own, that sounds quite fair to me, depends also on the lengths of those sequences. I think Mafft could be faster with some settings, but I have never aligned that many proteins. GPU is really good for speeding up numeric vector*matrix operations like in large neural networks or graphics rendering. Not sure if that would help here.