De novo assembler for single molecule sequencing reads using repeat graphs

Tools test whether admixture occurred and more

Phylogenetic orthology inference for comparative genomics

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

Software for painlessly estimating average nucleotide diversity within and between populations

Evolutionary Transcriptomics with R

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

A set of functions to visualise genotypes based on a VCF

Full-Length Alternative Isoform analysis of RNA

A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads

This is the development home of the workflow management system Snakemake. For general information, see

Automatically exported from code.google.com/p/cdhit

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

The Composer of ggplots

A flexible framework for rapid genome analysis and interpretation

🔬 BEDOPS: high-performance genomic feature operations

GFF and GTF file manipulation and interconversion

lumpy: a general probabilistic framework for structural variant discovery

Estimating Effective Migration Surfaces

Fast and frugal disk based k-mer counter

Ruby like string interpolation #{} in Python

Toolkit for processing sequences in FASTA/Q formats

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

A web wrapper for GeneValidator

GeneValidator: Identify problems with predicted genes

Modular and universal bioinformatics

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)