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 maintained by the nonprofit Phoenix Bioinformatics Corporation. It is co-developed by Phoenix Bioinformatics and the PANTHER project at University of Southern California, and is . Its initial development was 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

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4.1)

August 14November 15, 20202022. We are pleased to announce the PhyloGenes version 24.1release. This release .  updates only the GO annotation data and the publications counts for the gene family members. The gene families and gene trees are the same as for the PhyloGenes 4.0 release and are still from the  PANTHER 1517.0 release.  In PhyloGenes only  genes from plant genomes and selected non-plant model organisms were included. Genes from other genomes in the PANTHER build have been removed (pruned).  More stats

Updated GO annotations: Experimental gene function data was annotations were extracted from the Gene Ontology Consortium (files created on 2020-04-28by PANTHER on 2022-10-27, based on the 2022-07-01 GO release). Phylogenetic inferred gene function data was annotations were extracted from the  GO 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:

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(generated on 2022-09-26, based on the 2022-07-01 GO release which uses PANTHER 15 tree information, downloaded by the PhyloGenes team on 2022-10-20).

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