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SMURF

Source code to accompany: End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman See: https://www.biorxiv.org/content/10.1101/2021.10.23.465204v1

[1] Petti S, Bhattacharya N, Rao R, Dauparas J, Thomas N, Zhou J, Rush AM, Koo PK, Ovchinnikov S. End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. BioRxiv. 2021 Oct 24.

Source code for SSW and SMURF:

examples/SSW_examples: example usage and speed tests for SSW (Smooth Smith-Waterman):

examples/SMURF_examples: example usage of SMURF on RNA and protein and creation of associated figures

examples/LAM_AF_examples: example usage of LAM with AF and creation of associated figures