TreeFam: 2008 Update

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2007 Dec 7

PMID 18056084

Citations 211

Authors

Jue Ruan

Heng Li

Zhongzhong Chen

Avril Coghlan

Lachlan James M Coin

Yiran Guo

Jean-Karim Heriche

Yafeng Hu

Karsten Kristiansen

Ruiqiang Li

Tao Liu

Alan Moses

Junjie Qin

Soren Vang

Albert J Vilella

Abel Ureta-Vidal

Lars Bolund

Jun Wang

Richard Durbin

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

A pan-gene catalogue of Asian cultivated rice.

Contreras-Moreira B, Sharma E, Saraf S, Naamati G, Gupta P, Elser J bioRxiv. 2025; .

PMID: 40027622 PMC: 11870543. DOI: 10.1101/2025.02.17.638606.

A metric and its derived protein network for evaluation of ortholog database inconsistency.

Yang W, Ji J, Fang G BMC Bioinformatics. 2025; 26(1):6.

PMID: 39773281 PMC: 11707888. DOI: 10.1186/s12859-024-06023-x.

Population genetic differentiation and structure of rare plant Anemone shikokiana based on genotyping-by-sequencing (GBS).

An K, Zhou C, Tong B, Liu D, Shan X, Zhang X BMC Plant Biol. 2024; 24(1):995.

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Conserved role for spliceosomal component PRPF40A in microexon splicing.

Choudhary B, Norris A RNA. 2024; 31(1):43-50.

PMID: 39389624 PMC: 11648925. DOI: 10.1261/rna.080142.124.

Conserved role for spliceosomal component PRPF40A in microexon splicing.

Choudhary B, Norris A bioRxiv. 2024; .

PMID: 39386728 PMC: 11463390. DOI: 10.1101/2024.09.26.615222.

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