PhyloGenes 1.0

We are pleased to announce the initial launch of Phylogenes.org and the PhyloGenes version 1.0 release (released on April 2, 2019).  A total of 8173 gene families are included in this release. The gene families and gene trees are pruned versions of PANTHER 14.0 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). Experimental gene function data are extracted from the files available from the Gene Ontology Annotations (GOA) project at the EBI (file generated on 2018-12-03). More stats

PhyloGenes 1.1

We are pleased to announce the PhyloGenes version 1.1 release (released on August 1, 2019).  A total of 8171 gene families are included 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). Experimental gene function data are extracted from the files available from the Gene Ontology Annotations (GOA) project at the EBI (file generated on 2019-07-01). More stats

Highlights of new features of PhyloGenes gene tree display:

• Toggle between a compact view and a fully expanded view
• Remove  (prune) selected organisms from a gene tree
• Tree images can be downloaded as PNG or SVG files
• Gene trees can be downloaded in PhyloXML format
• Gene data tables can be downloaded as csv files

PhyloGenes 1.2

We are pleased to announce the PhyloGenes version 1.2 release (released on November 8, 2019).  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)

We enhanced the alignment between trees and their adjacent gene information tables. Leaf nodes in a tree now stay aligned with their corresponding gene rows in the gene table when resizing to a narrow browser window. We also fixed a rare data bug where some members were missing from the DUF641 gene family tree. If you notice anything else wrong please let us know!