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    20 repositories

    • partial_sampling_spatially_structured_population

      Public
      Repository for my lab immersion on spatially structured populations with partial updates.
      Jupyter Notebook
      •0•1•0•0•Updated Nov 7, 2024Nov 7, 2024

    • ProtMamba-ssm

      Public
      ProtMamba: a homology-aware but alignment-free protein state space model
      Jupyter Notebook
      •
      Apache License 2.0
      •7•49•2•0•Updated Oct 28, 2024Oct 28, 2024

    • fitness-landscapes

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • DrugRes_StructPop

      Public
      Repository for "Spatial structure facilitates evolutionary rescue by cost-free drug resistance" (2024) by C. Fruet, E. L. Müller, C. Loverdo, and A.-F. Bitbol.
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 2, 2024Sep 2, 2024

    • Phylogeny-ESM2

      Public
      Monte-Carlo generation of synthetic multiple sequence alignments along phylogenetic trees using a protein language model
      Python
      •0•0•1•0•Updated Jun 29, 2024Jun 29, 2024

    • ProtMamba-frozen-nips

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated May 22, 2024May 22, 2024

    • DiffPaSS

      Public
      Differentiable Pairing using Soft Scores
      Jupyter Notebook
      •
      Apache License 2.0
      •1•1•2•0•Updated May 20, 2024May 20, 2024

    • Phylogeny-sector-inference

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 19, 2024Apr 19, 2024

    • Structured_pop

      Public
      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.
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Feb 6, 2024Feb 6, 2024

    • Iterative_masking

      Public
      Iterative masking algorithm on MSA Transformer to generate synthetic sequences
      Jupyter Notebook
      •
      Apache License 2.0
      •7•22•0•0•Updated Jan 17, 2024Jan 17, 2024

    • Cooperation_structured_pop

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • DiffPALM

      Public
      Differentiable Pairing using Alignment-based Language Models
      machine-learningbioinformaticsprotein-sequenceslanguage-modelprotein-protein-interactionmultiple-sequence-alignmentprotein-structure-prediction
      Jupyter Notebook
      •
      Apache License 2.0
      •3•17•2•0•Updated Jan 5, 2024Jan 5, 2024

    • alphafold

      Public
      Open source code for AlphaFold.
      Python
      •
      Apache License 2.0
      •2.3k•0•0•0•Updated Dec 19, 2023Dec 19, 2023

    • T4P-T6SS-interplay

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 1, 2023Nov 1, 2023

    • DiffTrees

      Public
      Python
      •0•0•0•0•Updated Sep 27, 2023Sep 27, 2023

    • esm

      Public
      Evolutionary Scale Modeling (esm): Pretrained language models for proteins
      Python
      •
      MIT License
      •642•0•0•0•Updated Aug 10, 2023Aug 10, 2023

    • Phylogeny-MSA-Transformer

      Public
      Supporting repository for "Protein language models trained on multiple sequence alignments learn phylogenetic relationships" (https://www.nature.com/articles/s41467-022-34032-y)
      Jupyter Notebook
      •
      MIT License
      •2•16•0•0•Updated Mar 24, 2023Mar 24, 2023

    • Phylogeny-contact-inference

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 4, 2023Jan 4, 2023

    • Phylogeny-Partners

      Public
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Apr 24, 2022Apr 24, 2022

    • swalign

      Public
      Smith-Waterman local aligner
      Python
      •
      Other
      •22•0•0•0•Updated Nov 29, 2021Nov 29, 2021