phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly...2358 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the...ontact matrix as input and predicts the topologically associating domains and chromat...2338 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...2255 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to j...repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into...2246 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo ...e J#. Chromosome-scale scaffolding of de novo genome assemblies based on chromat...2193 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...2192 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genomes...amples of the various output types, see the CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.ht...2156 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and...ssification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, 13. do...2106 days ago
2042 days ago
Biotite: A general framework for computational biology
The package is open source and freely available at GitHub (https://github.com/biotite-d.... The Biotite package bundles popular tasks in computational biology into an unifying framework, w...1975 days ago