CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of diff...evolutionized the field of bioinformatics, and is currently implemented in all free an...2490 days ago
2349 days ago
Mash: fast genome and metagenome distance estimation using MinHash
Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other oper...2349 days ago
SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, nam...2341 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenk...l., Cell Systems, 2016), as well as additional dependencies noted below. Feel free to...2334 days ago
mojolicious: a next generation web framework for the Perl programming language.
Back in the early days of the web, many people learned Perl because of a wonderful Perl library called CGI....nstalled) Fresh code based upon years of experience developing Catalyst, free an...2318 days ago
GenomeTools: The versatile open source genome analysis software
The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary na...2293 days ago
An Introduction to Applied Bioinformatics
IAB is primarily being developed by Greg Caporaso(GitHub/Twitter: @gregca...Lab at Northern Arizona University. You can find information on the courses I teach on my teaching w...2270 days ago
Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses...2264 days ago
G-compass: a comparative genome browser
G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily... and its subdatabase Evola, respectively. G-compass is available for free of...2229 days ago