Overview

With increasing numbers of eukaryotic genome sequences, phylogenetic profiles of eukaryotic genes are becoming increasingly informative. PhyloPro exploits 120 available eukaryotic genome sequences to allow users to visualize the evolutionary trajectories of defined subsets of model organism genes. Applied to pathways or complexes, PhyloPro allows the user to rapidly identify core conserved elements of biological processes together with those that may represent lineage specific innovations. While PhyloPro is not meant as a replacement for detailed phylogenetic analyses, PhyloPro nonetheless serves to provide an intuitive web-based resource for performing rapid evolutionary and comparative studies of biological systems.

Focusing on the six model organisms: Arabadopsis thaliana (plant), Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), Drosophila melanogaster (fly), Mus musculus (mouse) and Homo sapiens (human), the Inparanoid algorithm was used to identify putative orthologs in 120 eukaryotes, including 5 plants, 30 protozoa, 26 fungi, 2 'basal' metazoa, 7 nematodes, 17 arthropods, 2 chordates, 7 vertebrates, and 24 mammals. For each of the query genes, five possible orthology relationships are defined:

No detectable ortholog (black)
1:1 - a single query gene has a single ortholog in the target species (dark yellow)
1:M - a single query gene has two or more orthologs in the target species (light yellow)
M:1 - a query gene together with at least one additional paralog are orthologs of a single gene in the target species (dark blue)
M:M - a query gene together with at least one additional paralog are orthologs of at least two orthologs in the target species genome (light blue)

PhyloPro is simple to use, and can be completed in only five steps: (1) input of query genes; (2) selection of target species; (3) data retrieval and clustering; (4) visualization; and (5) data download. Further details of its operation and examples of its application are provided in the Documentation and Application sections respectively.

Note due to the use of Canvas in HTML5, PhyloPro provides full functionality only for the following browser versions: Firefox 3.1+, Chrome 2.0+, Safari 4.0+, Opera 10.50+, and IE 9.0+ - earlier version browsers will have only limited functionality with the visualization interface.