PhyloGenes is a web resource that displays pre-computed phylogenetic trees of gene families alongside experimental gene function data to facilitate inference of unknown gene function in plants.
PhyloGenes is managed by the nonprofit Phoenix Bioinformatics Corporation. It is co-developed by Phoenix Bioinformatics and the PANTHER project at University of Southern California, and is supported by funding provided by the National Science Foundation (Grant No. DBI-1661543).
Current release (version 2.
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March 4August 14, 2020. We are pleased to announce the PhyloGenes version 2.01 release. A total of 8512 gene families are included in this release. The gene families and gene trees are pruned versions of from the PANTHER 15.0 release. They contain In PhyloGenes only genes genes from plant genomes and selected non-plant model organisms were included. Genes from other genomes in the PANTHER build have been removed (pruned). Experimental More stats
Experimental gene function data are was extracted from the files available from the Gene Ontology Annotations (GOA) project at the EBI (file generated on 2020-02-07). More stats
What’s new:
- 10 more plant genomes were added to gene families including potato, cassava, oilseed rape (see complete species list here)
- You can select an organism to have its genes highlighted in a tree
- Easier tree browsing using mouse wheel or trackpad for scrolling
- Better alignment between a tree and its gene information table
- Compact UI showing more data on a family page
- Safari and Firefox browsers are now supported
In the pipeline:
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Consortium (files created on 2020-04-28). Phylogenetic inferred gene function data was extracted from the PAINT project (files created on 2020-05-21).
What’s new:
- We added experimentally validated gene function annotations from GO Biological Process
- We added phylogenetic inferred gene functions (GO Biological Process and Molecular Function)
- Added feature to customize Gene information display to show/hide selected data and reorder columns. More details
What we are working on:
- Linking publications to genes in tree
- Download protein sequences of family members
Please take a few minutes to share with us your experience of using the PhyloGenes resource.