bioinformatics

Per-base per-nucleotide depth analysis

Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

A robust and fast clustering method for amplicon-based studies

Protein and molecule viewer, editor, simulator

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

machine learning for genomic variants

dbSNP

A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GA...

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

Analysis of immune repertoire sequencing results

Global Biotic Interactions provides access to existing species interaction datasets

Benchmark for LLM-based Agents in Computational Biology

FABind: Fast and Accurate Protein-Ligand Binding (NeurIPS 2023)

Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all

Global alignment and alignment extension

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

Open-source usearch

Calculation of interatomic interactions in molecular structures

Deep Learning-based Clustering Approaches for Bioinformatics

A high-performance, pure Rust toolkit for standardizing and preparing biomolecular systems (proteins & nucleic acids). It heals missing atoms, resolve...

Bam Error Stats Tool (best): analysis of error types in aligned reads.

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive b...

Software for biomolecular electrostatics and solvation calculations

Analyze your RNA sequencing data without writing a single line of code

An efficient FASTQ manipulation suite

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

PANDORA :computer:

Plasmid and primer design software

Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.

BWA-MEME: Faster BWA-MEM2 using learned-index

Tools for single-cell data processing

Extract 3D contacts (.pairs) from sequencing alignments

Bayesian genotyper for structural variants

Base Classes and Functions for Mass Spectrometry and Proteomics

GATK RNA-Seq Variant Calling in Nextflow

Comparative Genomics Toolkit 3

Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)

Parser and database to index the terpene profile of different strains of Cannabis from online databases

An open-access bioinformatics text

A minimalist multi-agent framework for rubost automation of scientific analysis workflows, such as gene expression analysis.

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

python library for working with ontologies and ontology associations

MyGene.info: A BioThings API for gene annotations

APBS - software for biomolecular electrostatics and solvation

Gene fusion detection and visualization

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

An app store for scientific workflows, tools, notebooks, and services

:rocket: seqfu - Sequece Fastx Utilities

A universal infrastructure layer for generative biology