Phylogenetic Annotation Project

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PAINT : Software for tree annotation

The reference project group has developed a software to perform the annotations based on phylogenetic trees.

PAINT Curation guidelines

Please contact PAINT team to have access to the document.


Scripts to ensure PAINT data integrity

PAINT annotation SOPs

GAFs for trees-based annotations

Standard Operating Procedure for Tree-based propagation of annotations

Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements

Orthology determination

Data used to make orthology calls

reference proteomes files

At the July 2009 Quest for Orthologs meeting, it was agreed to decide upon a standard set of genomes, and compile "complete" sets of protein coding genes for each genome, and a representative protein sequence for each gene.

New gene2geneproduct file

At the April 2009 Reference Genome meeting it was decided to create a new file to replace the GP2protein file, called 'gene2geneproduct'. Specifications can be found on this page (will be added soon).


Software/database development


The purpose of this page is to discuss features and requirements that would be desirable in a database used to replace the existing Google Spreadsheet system for managing target genes, their annotations and metrics.


Archived & retired Pages

Preretired pages! To discuss with DH and KVH


Gene pages

http://wiki.geneontology.org/index.php/Category:Reference_Genome_Genes > I forgot how those were created. They can probably all be removed. Can this be done in bulk?


Retired Pages

Those pages are kept as reference but the information in them is not the most current information.

Past Annotation targets