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...1607 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacenc...RT-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside gen...1580 days ago
Mercator: Multiple Whole-Genome Orthology Map Construction
Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genom...1443 days ago
ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome bac...1388 days ago
Sibelia: A comparative genomics tool
...correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement stud...1349 days ago
G-NEST: The Gene NEighborhood Scoring Tool
The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository.1314 days ago
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
...steps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny. The new R package targets ecology, population and evolutionary biologists working in the fie...1267 days ago
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...793 days ago
OneZoom tree of life explorer...
An interactive map of the evolutionary links between all living things known to science. Discover your favourites, see which species are under threat, and be amazed by the diversity of life on earth.537 days ago
OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users from over 60 countries.366 days ago