As some of you will already be aware, the Xfam family has recently gained a new member: the TreeFam database.
TreeFam aims to provide phylogenetic trees and orthology predictions for all animal genes.
What is TreeFam ?
TreeFam (http://www.treefam.org/) provides the scientific community with manually curated and automatically generated phylogenetic trees for animal genes.
TreeFam is also an ortholog database. Unlike other pairwise alignment based resources, TreeFam infers orthologs using gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and gene losses. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.
To read more about how TreeFam works, you can have a look at either of the two previously published papers
- Original publication
- TreeFam Update paper
or Heng Li’s PhD thesis.
The people behind TreeFam ?
TreeFam started in 2004 as a collaboration between Richard Durbin’s group at Sanger and the Beijing Genome Institute (BGI). The following years saw several releases of the TreeFam database (the previous release was TreeFam 7, on 10th February 2009 with 777,321 genes in 16,141 families).
Many people have contributed to making TreeFam a valuable resource for studying the evolution of animal genes. Among others, these were:
- Heng Li (now at the Broad Institute, Congratulations on winning the Benjamin Franklin Award),
- Jue Ruan
- Avril Coghlan (now at University College Cork)
- Jean-Karim Heriche (now at the EMBL, Heidelberg)
- Javier Herrero (EBI)
- Albert Viella (EBI)
- Ensembl team
- Richard Durbin (Sanger Institute)
- Jun Wang (BGI)
- Alex Bateman (has taken over the TreeFam management from Richard Durbin)
- Fabian Schreiber (new TreeFam project leader)
Version 8 and future releases
We have released a new TreeFam version. It is TreeFam 8 with 1,539,621 genes and 16,064 families mainly based on Ensembl 54. This version was built by Jue Ruan in 2009, but had never gone online.
Although TreeFam 8 is not built from the latest Ensembl release, we thought it might be a good idea to make this release available to the scientific community. You can see TreeFam 8 as a sign of life, that the TreeFam database is not dead and that there are great things to come.
Over the coming months, we will keep you updated with TreeFam news on this blog while heavily working on making a cool new release available.
Posted by Fabian