entity-nucleic-acid

C library for high-throughput sequencing data formats

Toward High-Accuracy Open-Source Biomolecular Structure Prediction.

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Code for the DISCO model: General Multimodal Protein Design Enables DNA-Encoding of Chemistry

Protein and nucleic acid validation service

Source code for molecular graphics program UCSF ChimeraX

bedtools - the swiss army knife for genome arithmetic

Oxford Nanopore's Basecaller

Tools (written in C using htslib) for manipulating next-generation sequencing data

A dependency-free cross-platform swiss army knife for PDB files.

Reduce - tool for adding and correcting hydrogens in PDB files

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

IQ-TREE software version 2: phylogenetics by maximum likelihood

Official repository for the Boltz biomolecular interaction models

Foundation Models for Genomics & Transcriptomics

A comprehensive library for computational molecular biology

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Official code repository for GATK versions 4 and up