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...1623 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
...ighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled acc...istical supports on ancestral and extant adjacencies are provided. DeC...DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fissio...1597 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 "synte...term is incorrect (Passarge et al. 1999) and thus we will use the terms "homologous...as paralogous regions within each genome and hypoth...1460 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 h...1404 days ago
Sibelia: A comparative genomics tool
Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlat...nisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome...1365 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.1331 days ago
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 20...ocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps fr..., codon alignments to Ka/Ks calculations and synteny. The new R package targets ecology, population and evolutiona...1283 days ago
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...809 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.553 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.382 days ago