FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing

ULTRA Locates Tandemly Repetitive Areas

TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments

Gene fusion detection and visualization

Toolbox to visualise the transposable element landscape of several species at a time by using data from RepeatMasker and TESorter

Linking phenotypic and genotypic variation: a relaxed phylogenetic approach using the probabilistic programming language Stan

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Tools and scripts to build synteny blocks from chains and nets

Scripts from the waterbuck paper

Scripts and datasets for the analysis on convergent genome evolution of animal terrestrialisation

A package to count reads mapping on transposable elements subfamilies, families and classes.

Structural variant caller for real-time long-read sequencing data

SPAdes Genome Assembler

Taxonomy addition for complete trees

BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools. Actively maintained by Brian Bushnell.

Pair-End AssembeR

Prior-Oblivious Length Estimation in Genealogies with Oriented Network

A package to make streamplots

A geom for ggplot to create bump plots

fork of the GPU genome aligner

R package constellatoR to check functional convergence in long lists of Gene Ontology terms and orthogroups

Synteny and Rearrangement Identifier

The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.

Bioinformatics pipeline and tutorial for performing gene annotation in genome assemblies using GALBA

Bioinformatics pipeline and tutorial for performing repeat annotation in genome assemblies using RepeatModeler and RepeatMasker.