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Protein families, Orthologs and Paralogs from Phytozome.
Current data
Phytozome Families
All proteins from the Phytozome database are grouped into a hierachical structure of related polypeptide sequence. A family consisting of more than one protein also has a computed multiple sequence alignment (MSA) and computed centroid sequence.
Ortholog/Paralog Data
Phytozome has compiled a collection orthologs and paralogs for the genes in our database.

Ortholog calls were generated using inParanoid 4.1. InParanoid was run on proteome sequences for all possible organism-organism pairs in Phytozome using the default two-pass blast strategy. Genes from different species that fell in the same InParanoid ortholog cluster were considered orthologs.

The scale of the homolog data makes it impractical to store in our InterMine database. You can best query for homologs of a gene or set of genes by using our BioMart interface.

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Remm M, Storm CE and Sonnhammer EL. J. Mol Biol. 2001 Dec 14.

Bulk download
Bulk data files for all organisms in Phytozome are available for download from the JGI Download Portal .
Related template queries
Query starting points

These links will take you to the Query Builder pages which allow you to make new queries and create template queries of your own