406 Open source projects that are alternatives of or similar to ensembl-compara

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

🔬 Assemble large genomes using short reads

A genome browser that shows long reads and complex variants better

Rapid large-scale prokaryote pan genome analysis

RAxML Next Generation: faster, easier-to-use and more flexible

Examples of using deep learning in Bioinformatics

Toolset for SV simulation, comparison and filtering

JavaScript VisualizationTools

A curated list of resources for learning bioinformatics.

Annotated data.

Syntax highlighting for computational biology

Python package for graph neural networks in chemistry and biology

Quickly search, compare, and analyze genomic and metagenomic data sets.

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

Deep learning infrastructure for bioinformatics

Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.

Reads simulator

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

React component for Cytoscape.js network visualisations

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Core BioPerl 1.x code

Proof-of-concept seq-to-graph mapper and graph generator

The sources of the openSNP website

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

A powerful open source data warehouse system

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

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

Haplotype VCF comparison tools

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

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

GenomeTools genome analysis system.

This is the ensembldb development repository.

Protein Graph Library

Remote protein homology detection suite.

Python for Bioinformatics

A curated list of Cheminformatics libraries and software.

Ten Quick Tips for Deep Learning in Biology

An ultrafast memory-efficient short read aligner

Genome assembly evaluation tool

A simple command-line tool to download data from Joint Genome Institute databases

Cuneiform distributed programming language

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Curated (meta)list of resources for Biology.

Official git repository for Biopython (originally converted from CVS)

A repository for setting up a RNAseq workflow

🔬 BEDOPS: high-performance genomic feature operations

Tools for working with genomic and high throughput sequencing data.

A tool for analysis of assembly graphs

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Bioconductor cheat sheet

cython + htslib == fast VCF and BCF processing

BioGrakn Knowledge Graph

code for reading and processing Allen Institute for Brain Science data

A faster lmm for GWAS. Supports GPU backend.

Federating genomes with love (and synteny derived from functional annotations)

Structural variation caller using third generation sequencing

Strelka2 germline and somatic small variant caller