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 seve...axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has...to the genomic context of all its orthologous and paralo...2373 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 pro...uch as taxonomic information, gene names and identifi...operability between various applications and databa...2362 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that...present at different levels of the NCBI taxonomy, and then to collect reads from th...roduces evolved sequences based on source genomes and a given evolutiona...2357 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...ude (i) building gene-based and supermatrix-based phylogenies...(ii) testing and visualizing evolutionary models, (iii) calculating d...2280 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 maximum likelih...2265 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 a drawing...2264 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 some of its...2258 days ago
Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed for...improve the accuracy of variant calling results and to infer the evolutionary history of the organismĀ“s gen...evaluating of the assemble haplotypes by gold standard (lo...2178 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://mula...ional elements conserved over evolutionary time. Mulan brings t...local sequence conservation, and the multiTF program for detecting evol...GALA can be viewed in Mulan, and conser...2094 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 ReadTheDocs1792 days ago