cuda-accelerated sequence alignment program

Question

[sunyeping]

Dear all,

I want to do protein sequence alignment with a very large dataset which contains over 130,000 sequences. Could you recommend some cuda-accelerated sequence alignment software? I find there is a cuda-mafft, the cuda-accelerated mafft, but I don't know where to download the code. Do you know where to find the code for it? Or what are the better alternatives?

Thank you in advance.

[Joe]

I have no experience with any of these (much less GPU alignment in general), but from a quick google:

• https://github.com/edanssandes/MASA-CUDAlign
• https://sourceforge.net/projects/cudalign/
• https://github.com/coldfunction/CUDA-clustalW
• https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190279
• http://seqbarracuda.sourceforge.net/