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

...

4.

...

1)

March 4November 15, 20202022. We are pleased to announce the PhyloGenes version 24.0.  A total of 8512 gene families are included in this release1 release. This release updates only the GO annotation data and the publications counts for the gene family members. The gene families and gene trees are pruned versions of PANTHER 15are the same as for the PhyloGenes 4.0 release and are still from the PANTHER 17.0 release.  They contain only genes from plant genomes and selected non-plant model organisms. Genes from other genomes in the PANTHER build have been removed (pruned).  Experimental More stats

Updated GO annotations: Experimental gene function data are annotations were 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:

• Display gene function annotations to GO Biological Process terms that are supported by experimental evidence
• Display inferred gene functions through biological ancestor
• Download Multiple Sequence Alignment of gene families
• Download protein sequences of family members

===archive the following ===

Current release (version 1.2)

The gene family build has not changed in this release. The gene families and gene trees are pruned versions of PANTHER 14.1 release. They contain only genes from selected plant genomes and 10 non-plant model organisms. Genes from other genomes in the PANTHER build have been removed (pruned). More stats

What's new:

• Experimental gene function data have been updated. They were extracted using the QuickGO REST API (https://www.ebi.ac.uk/QuickGO/api/index.html) on 2019-10-25.
• Toggle to see multiple sequence alignment (MSA) of a gene family (more)
• Graft your sequence to an existing PhyloGenes gene family tree (for species not included in PhyloGenes) (more)

In the pipeline:

...

Consortium (files created by PANTHER on 2022-10-27, based on the 2022-07-01 GO release). Phylogenetic inferred gene function annotations were extracted from the GO PAINT project (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).

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