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alphafold

Open source code for AlphaFold.

cooperation_structured_pop

diffpalm

Differentiable Pairing using Alignment-based Language Models

diffpass

Differentiable Pairing using Soft Scores

difftrees

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

fitness-landscapes

iterative_masking

Iterative masking algorithm on MSA Transformer to generate synthetic sequences

phylogeny-contact-inference

phylogeny-esm2

Monte-Carlo generation of synthetic multiple sequence alignments along phylogenetic trees using a protein language model

phylogeny-msa-transformer

Supporting repository for "Protein language models trained on multiple sequence alignments learn phylogenetic relationships" (https://www.nature.com/articles/s41467-022-34032-y)

phylogeny-partners

phylogeny-sector-inference

protmamba-frozen-nips

protmamba-ssm

ProtMamba: a homology-aware but alignment-free protein state space model

structured_pop

This repository provides the python code used to generate Figures in articles "Frequent asymmetric migrations suppress natural selection in spatially structured populations" , and "Mutant fate in spatially structured populations on graphs: connecting models to experiments" by A. Abbara, L. Pagani, C. García-Pareja, and A.-F. Bitbol.

swalign

Smith-Waterman local aligner

t4p-t6ss-interplay