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...2362 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows f.... The simulation stage uses the model built in the previous step to produce in silico...2343 days ago
CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distr...lows to simultaneously work with scaffold assemblies obtained from any in silico&...2333 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...2258 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...2250 days ago
Digest: In silico restriction digest of complete genomes
This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragmen...2196 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...2195 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...2159 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), a...assification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, 13. do...2109 days ago
2045 days ago