Genomicus: genome browser that enables users to navigate in genomes in several dimensions
...s to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has...2360 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 use...2349 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
...f a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree.2345 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
.... The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating d...2268 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 ma...2253 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...2251 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 anal...2246 days ago
Ranbow: a haplotype assembler for polyploid genomes
...id genomes. After a first phasing, Ranbow utilizes the assembled haplotypes to improve the accuracy of variant calling results and to infer the evolutionary history of the organismĀ“s gen...2166 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
...a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together s...2081 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 ReadTheDocs1780 days ago