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
☆10Updated last month
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.☆92Updated 3 months ago
- An implementation of ESM2 in Equinox+JAX☆35Updated 4 months ago
- My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other h…☆54Updated 2 years ago
- Benchmark for LLM-based Agents in Computational Biology☆54Updated this week
- Mol* as anywidget☆40Updated 4 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…☆98Updated 2 years ago
- Functions and classes for doing Gaussian process models of proteins☆11Updated 7 years ago
- Causal and probabilistic reasoning with continuous time dynamical systems☆19Updated last month
- Differentiable RNA folding in JAX☆22Updated 6 months ago
- Interpretable genotype-phenotype landscape modeling☆35Updated last year
- Your favourite classical machine learning algos on the GPU/TPU☆20Updated 9 months ago
- Minimal AlphaFold☆54Updated last year
- The project proposal template for OpenBioML community projects.☆18Updated 2 years ago
- Tokenizers and Machine Learning Models for biological sequence data☆25Updated last year
- The full training script for Enformer - Tensorflow Sonnet☆18Updated 3 years ago
- JAX translation of boltz☆20Updated 2 months ago
- A standard library for biological research.☆29Updated last month
- Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders☆223Updated last week
- MaxEnt code for fitting simulation outcomes/statistical models to observations☆16Updated 3 years ago
- pyGPCCA - python GPCCA: Generalized Perron Cluster Cluster Analysis package to coarse-grain reversible and non-reversible Markov state mo…☆22Updated 6 months ago
- [ICML 25] We train and evaluate SAEs to identify interpretable features in pLMs and show their potential for scientific discovery.☆118Updated this week
- DImensionality REduction in JAX☆24Updated 3 weeks ago
- ☆25Updated 3 years ago
- Diverse Genomic Embedding Benchmark☆47Updated last month
- ☆36Updated 11 months ago
- ☆30Updated 2 years ago
- Equivariant layers for RC-complement symmetry in DNA sequence data☆11Updated 3 years ago
- ☆17Updated 11 months ago
- A repository with exploration into using transformers to predict DNA ↔ transcription factor binding☆85Updated 3 years ago
- Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AI…☆35Updated 3 years ago