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).


Citing PhyloGenes: 

PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference 

Zhang P, Berardini TZ, Ebert D, Li Q, Mi H, Muruganujan A, Prithvi T, Reiser L, Sawant S, Thomas PD, Huala E

Plant Direct. 2020 Dec;4(12):e00293


Current release (version 3.2)

September 21, 2021. We are pleased to announce the PhyloGenes version 3.2 release. The gene families and gene trees are not changed in this release. They are still based on the PANTHER 16.0 release. As always in PhyloGenes, only genes from plant genomes and selected non-plant model organisms were included and genes from other genomes in the PANTHER build have been removed (pruned). More stats


Updated GO annotations: Experimental gene function data was extracted from the Gene Ontology Consortium (files created on 2021-07-19). Phylogenetically-inferred gene function data was extracted from the PAINT project (files created on 2021-07-19).


Improved user interface and user experience: This release features enhanced technology behind our gene family pages. Page loading and scrolling are now faster and smoother for large gene trees that also have extensive number of GO annotations to the family members. For an even better site experience, we recommend that users  use the on-the-fly tree pruning and gene table customization options. Customization not only speeds up the page loading time but also allows you to focus on the species of interest and the GO functional aspects most relevant to your study.


New! Publications now available!: Extensive publication lists for individual family members can now be accessed via hyperlinks from the gene information table. The publication counts are retrieved from UniProt via their API and will be updated on a quarterly basis.


Please take a few minutes to share with us your experience of using the PhyloGenes resource. 


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