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 4.0)

May 11, 2022. We are pleased to announce the PhyloGenes version 4.0 release. The gene families and gene trees are from the PANTHER 17.0 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 annotations were extracted from the Gene Ontology Consortium (files created on 2022-01-13). Phylogenetic inferred gene function annotations were extracted from the GO PAINT project (downloaded on 2022-03-22, based on the 2022-01-13 GO release which uses PANTHER 15 tree information).

Improved user interface and user experience: We have split out functionality for Downloads from Tools into two separate menus to make these actions clearer and more easily accessible. We have also introduced wording to suggest pruning a tree to a subset of species when accessing trees that contain more than 500 sequences. The pruned view will give each user a customized view of their gene family and a faster page load time.

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

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