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

Visualization and analysis software for Hi-C data -

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Accurate Species TRee ALgorithm

Bayesian Evolutionary Analysis by Sampling Trees

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

Jasmine: SV Merging Across Samples

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

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…