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Repository for Protein-Vec, a protein embedding mixture of experts model
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Non-sequential structural alignment program for protein structure
Compressing protein structures effectively with torsion angles
Universal Structure Alignment of Monomeric and Complex Structure of Nucleic Acids and Proteins
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
Python package to manage protein structures and their annotations
Foldseek enables fast and sensitive comparisons of large structure sets.
Refinements of the WFA alignment algorithm with better complexity
Making Protein folding accessible to all!
Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.
Implementation of Invariant Point Attention, used for coordinate refinement in the structure module of Alphafold2, as a standalone Pytorch module
Open source code for AlphaFold.
Bonsai: Fast, flexible taxonomic analysis and classification
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.
Reconstruction of phylogenetic insertion-deletion histories
Get protein embeddings from protein sequences
PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF files with PhyloCSF and confidence scores.
Mapping NCBI Genbank accession to GTDB accession