gata-bio / affine-gapsLinks
Less-wrong single-file Numba-accelerated Python implementation of Gotoh affine gap penalty extensions for the Needleman–Wunsch, Smith-Waterman, and Levenshtein algorithms for sequence alignment
☆9Updated 2 months ago
Alternatives and similar repositories for affine-gaps
Users that are interested in affine-gaps are comparing it to the libraries listed below
Sorting:
- Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.☆83Updated 2 weeks ago
- An implementation of ESM2 in Equinox+JAX☆29Updated 3 weeks ago
- Minimal AlphaFold☆53Updated 10 months ago
- SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.☆19Updated last year
- JAX translation of boltz☆18Updated 2 weeks ago
- Benchmark for LLM-based Agents in Computational Biology☆44Updated 2 weeks ago
- My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other h…☆53Updated last year
- Parsing MHC nomenclature in the wild☆16Updated 3 months ago
- RITA is a family of autoregressive protein models, developed by LightOn in collaboration with the OATML group at Oxford and the Debora Ma…☆97Updated 2 years ago
- Mol* as anywidget☆39Updated 3 weeks ago
- ☆109Updated last month
- MaxEnt code for fitting simulation outcomes/statistical models to observations☆16Updated 3 years ago
- An efficient method for the conversion from internal to Cartesian coordinates that utilizes the platform-agnostic JAX Python library.☆17Updated last year
- Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AI…☆34Updated 3 years ago
- Jax code for functional genomics ML☆14Updated 3 months ago
- Epistatic Net is an algorithm which allows for spectral regularization of deep neural networks to predict biological fitness functions (e…☆18Updated 3 years ago
- Interpretable genotype-phenotype landscape modeling☆35Updated last year
- A Modular Architecture for Deep Learning Systems☆41Updated last month
- Functions and classes for doing Gaussian process models of proteins☆11Updated 7 years ago
- Python framework for multi-parameter optimization and evaluation of protein folding models☆17Updated 4 years ago
- ☆25Updated 3 years ago
- The project proposal template for OpenBioML community projects.☆18Updated 2 years ago
- Implementation of the Pairformer model used in AlphaFold 3☆12Updated 2 weeks ago
- Benchmarking common tasks on proteins in various languages and packages☆42Updated 4 years ago
- The full training script for Enformer - Tensorflow Sonnet☆18Updated 3 years ago
- ☆12Updated 9 months ago
- ☆14Updated 7 months ago
- ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers☆18Updated 6 months ago
- ML-guided enzyme engineering☆64Updated 2 weeks ago
- Implementation of Nvidia's NeuralPlexer, for end-to-end differentiable design of functional small-molecules and ligand-binding proteins, …☆51Updated last year