TreeFam: 2008 Update

By Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, L. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li and 9 more. Nucleic Acids Res., 2007

333 citations recorded by the source corpus.

TreeFam (http://www.treefam.org) was developed to provide curated phylogenetic trees for all animal gene families, as well as orthologue and paralogue assignments. Release 4.0 of TreeFam contains curated trees for 1314 families and automatically generated trees for another 14 351 families. We have expanded TreeFam to include 25 fully sequenced animal genomes, as well as four genomes from plant and fungal outgroup species. We have also introduced more accurate approaches for automatically grouping genes into families, for building phylogenetic trees, and for inferring orthologues and paralogues. The user interface for viewing phylogenetic trees and family information has been improved. Furthermore, a new perl API lets users easily extract data from the TreeFam mysql database.

Subfields: Ecological Modeling, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/23e43d2a848d70c18cf85428df74b326e89611b9

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Citations in the corpus

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic (2021, methodology): “Alternatively, new genome sequences could be contextualized by placing samples onto an existing ‘reference phylogeny’ and several methods have been developed for this purpose 17–20 .”
Phytozome: a comparative platform for green plant genomics (2011, methodology): “Gene family construction in Phytozome uses a distance-based approach similar to the PhiGs method (43), the initial proto-family creation step used in TreeFam, with several modifications (see Supplemental Methods 2).”
GREAT improves functional interpretation of cis-regulatory regions (2010, positive): “An enrichment analysis of TreeFam gene families 24 shows that SRF binds in proximity to five of six members of the FOS family.”
Ensembl 2014 (2013, methodology): “In close collaboration with the TreeFam (39) and Ensembl Genomes (10) projects, we will migrate to an HMM-based classiﬁcation for GreeTree annotation, which will reduce a key quadratic complexity to a linear one.”