RStudio is an integrated development environment (IDE) for R

Graphical Java application for managing BibTeX and BibLaTeX (.bib) databases

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

A quality control analysis tool for high throughput sequencing data

Java utilities for Bioinformatics

Genome-scale protein function classification

RTG Tools: Utilities for accurate VCF comparison and manipulation

ROBOT is an OBO Tool

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Visualization and analysis software for Hi-C data -

Accurate Species TRee ALgorithm

Bayesian Evolutionary Analysis by Sampling Trees

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

Bayesian Evolutionary Analysis Sampling Trees

Software for aligning viewing and editing dna/aminoacid sequences, intuitive, fast and lightweight. Download and website:

OWLTools

MinHash Alignment Process (MHAP, pronounced MAP): locality-sensitive hashing to detect long-read overlaps and utilities

Posterior summarisation in Bayesian phylogenetics

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various us…

Mapped QC analysis program

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological…

Taxonomy-aware DNA sequence processing toolkit

A small program that glues together other programs allowing a user to input a codon alignment in FASTA format and produce an annotated phylogenetic tree showing which substitutions occurred on a gi…