41 Open Source Bioinformatics Tool Software Projects

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

A modular annotation tool for genomic variants

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

⛓ Correct misassemblies using linked AND long reads

:hibiscus: reference-free transcriptome assembly for short and long reads

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

A collection of Web Service Clients to consume EBI's tools via REST and SOAP APIs.

Phigaro is a scalable command-line tool for predicting phages and prophages

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

MView extracts and reformats the results of a sequence database search or multiple alignment.

an implementation of NSGA-II in java

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.

MHC class II binding prediction

Bioinformatics Library for Pharo Smalltalk

:chains: Construct a Physical Map from Linked Reads

SOPanG, a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.

Fast and accurate prediction of coiled coil domains in protein sequences. ​

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

Genomics data visualization in Python by using matplotlib.

Blender plugin to process biological data and molecular work.

iLearnPlus is the first machine-learning platform with both graphical- and web-based user interface that enables the construction of automated machine-learning pipelines for computational analysis and predictions using nucleic acid and protein sequences.

:rocket: seqfu - Sequece Fastx Utilities

Large-scale automatic feature selection for biomarker discovery in high-dimensional OMICs data

A software to detect virome-wide integrations

Explore biomolecular pathways in Reactome from the command-line or a Python script

R package specialized in HLA typing clustering and visualization based on specific similarity metrics

fast and comprehensive k-mer counting package

Scissor package

MeShClust2: Application of alignment-free identity scores in clustering long DNA sequences

CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

GWAS summary statistics files QC tool

Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.