Genomicus: genome browser that enables users to navigate in genomes in several dimensions
Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chrono...2368 days ago
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 used fea...2357 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a datab...2352 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and...2275 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a m...2260 days ago
PhyloGrapher - Graph Visualization Tool
PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is...2259 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 phyloge...2253 days ago
Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranb...2173 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Mulan (http://mulan.dcode.org/), a novel method and a network server for compari...2089 days ago
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses
find the resources we provide here useful in getting you set up to analyse and interpret your data. To reference VESPA: https://peerj.com/preprints/1895/ Documentation is now hosted on ReadTheDocs1787 days ago