gata-bio / affine-gaps
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 last month
Alternatives and similar repositories for affine-gaps:
Users that are interested in affine-gaps are comparing it to the libraries listed below
- Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.☆82Updated this week
- Benchmark for LLM-based Agents in Computational Biology☆35Updated 2 weeks ago
- ☆13Updated 6 months ago
- Parsing MHC nomenclature in the wild☆16Updated last month
- Minimal AlphaFold☆53Updated 8 months ago
- The project proposal template for OpenBioML community projects.☆18Updated 2 years ago
- An implementation of ESM2 in Equinox+JAX☆25Updated 2 months ago
- Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AI…☆34Updated 3 years ago
- SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.☆19Updated last year
- Implementation of the Pairformer model used in AlphaFold 3☆12Updated this week
- Tokenizers and Machine Learning Models for biological sequence data☆25Updated 7 months ago
- Non-sequential structural alignment program for protein structure☆19Updated 6 months ago
- An efficient method for the conversion from internal to Cartesian coordinates that utilizes the platform-agnostic JAX Python library.☆17Updated 10 months ago
- the MAVISp database for annotations and predictions of variant effects at the protein level☆11Updated 3 weeks ago
- A standard library for biological research.☆25Updated this week
- PDBClean helps create a curated ensemble of molecular structures☆12Updated last month
- JAX translation of boltz☆13Updated 3 months ago
- MaxEnt code for fitting simulation outcomes/statistical models to observations☆16Updated 2 years ago
- ☆34Updated 8 months ago
- Jax code for functional genomics ML☆12Updated 2 months ago
- Interpretable genotype-phenotype landscape modeling☆35Updated last year
- My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other h…☆52Updated last year
- ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers☆18Updated 5 months ago
- SPECTRA: Spectral framework for evaluation of biomedical AI models☆38Updated 2 months ago
- Mol* as anywidget☆34Updated 3 weeks ago
- Printing text using protein structures☆13Updated 3 years ago
- Functions and classes for doing Gaussian process models of proteins☆11Updated 7 years ago
- Equivariant layers for RC-complement symmetry in DNA sequence data☆11Updated 3 years ago
- Benchmarking common tasks on proteins in various languages and packages☆41Updated 4 years ago
- RITA is a family of autoregressive protein models, developed by LightOn in collaboration with the OATML group at Oxford and the Debora Ma…☆96Updated 2 years ago