karyoploteR: plot whole genomes with arbitrary data
karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system...1965 days ago
MUMmer4: A fast and versatile genome alignment system
MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a...2297 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...2293 days ago
Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but s...2259 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to...e repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into...2251 days ago
MITObim - mitochondrial baiting and iterative mapping
This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full arti...comes with this Repo, just to make sure everything is running smoothly on your system....2204 days ago
GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.2178 days ago
Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Ci...s using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 1...2196 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genom...xamples of the various output types, see the CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.ht...2160 days ago
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto
NAViGaTOR – Network Analysis, Visualization, & Graphing TORonto is a software system for scaleable visualizing and analyzing networks. The current version, NAViGaTOR 3, increases modulari...2148 days ago