unum-bio / AffineGapsLinks
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 2 months ago
Alternatives and similar repositories for AffineGaps
Users that are interested in AffineGaps 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.☆98Updated 7 months ago
- An implementation of ESM2 in Equinox+JAX☆35Updated 7 months ago
- My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other h…☆55Updated 2 years ago
- DImensionality REduction in JAX☆24Updated 2 months ago
- Differentiable RNA folding in JAX☆27Updated 9 months ago
- Minimal AlphaFold☆56Updated last year
- 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
- Tokenizers and Machine Learning Models for biological sequence data☆25Updated last year
- The project proposal template for OpenBioML community projects.☆18Updated 2 years ago
- Equivariant layers for RC-complement symmetry in DNA sequence data☆11Updated 3 years ago
- Benchmark for LLM-based Agents in Computational Biology☆68Updated 3 months ago
- Interpretable genotype-phenotype landscape modeling☆36Updated 2 years ago
- Mol* as anywidget☆49Updated 3 months ago
- The full training script for Enformer - Tensorflow Sonnet☆18Updated 3 years ago
- Your favourite classical machine learning algos on the GPU/TPU☆20Updated last month
- ☆20Updated last month
- GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics☆139Updated 2 months ago
- ☆134Updated 3 years ago
- awesome tools for RNA☆17Updated 3 years ago
- Jax code for functional genomics ML☆14Updated 10 months ago
- Diverse Genomic Embedding Benchmark☆50Updated 4 months ago
- ☆25Updated 3 years ago
- [ICML 25] We train and evaluate SAEs to identify interpretable features in pLMs and show their potential for scientific discovery.☆123Updated this week
- A repository with exploration into using transformers to predict DNA ↔ transcription factor binding☆88Updated 3 years ago
- Evaluating RNA structure prediction using diverse thermodynamic prediction tasks and high-throughput datasets.☆17Updated 3 years ago
- Benchmarking common tasks on proteins in various languages and packages☆42Updated 5 years ago
- A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.☆41Updated 2 years ago
- Non-sequential structural alignment program for protein structure☆19Updated last year
- Evolution Pretraining Fully in Int Formats☆135Updated last month
- Functions and classes for doing Gaussian process models of proteins☆11Updated 7 years ago