TreeFam: 2008 Update

Jue Ruan; Heng Li; Zhongzhong Chen; Avril Coghlan; Lachlan James M Coin; Yiran Guo; Jean-Karim Hériché; Yafeng Hu; Karsten Kristiansen; Ruiqiang Li; Tao Liu; Alan Moses; Junjie Qin; Søren Vang; Albert J Vilella; Abel Ureta-Vidal; Lars Bolund; Jun Wang; Richard Durbin

doi:10.1093/nar/gkm1005

TreeFam: 2008 Update

Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin

214 Citations (Scopus)

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.

Original language	English
Book series	Nucleic Acids Symposium Series
Volume	36
Issue number	Database issue
Pages (from-to)	D735-D740
ISSN	0261-3166
DOIs	https://doi.org/10.1093/nar/gkm1005
Publication status	Published - 2008
Externally published	Yes

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title = "TreeFam: 2008 Update",

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.",

author = "Jue Ruan and Heng Li and Zhongzhong Chen and Avril Coghlan and Coin, {Lachlan James M} and Yiran Guo and Jean-Karim H{\'e}rich{\'e} and Yafeng Hu and Karsten Kristiansen and Ruiqiang Li and Tao Liu and Alan Moses and Junjie Qin and S{\o}ren Vang and Vilella, {Albert J} and Abel Ureta-Vidal and Lars Bolund and Jun Wang and Richard Durbin",

year = "2008",

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language = "English",

volume = "36",

pages = "D735--D740",

journal = "Nucleic acids symposium series",

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TY - JOUR

T1 - TreeFam: 2008 Update

AU - Ruan, Jue

AU - Li, Heng

AU - Chen, Zhongzhong

AU - Coghlan, Avril

AU - Coin, Lachlan James M

AU - Guo, Yiran

AU - Hériché, Jean-Karim

AU - Hu, Yafeng

AU - Kristiansen, Karsten

AU - Li, Ruiqiang

AU - Liu, Tao

AU - Moses, Alan

AU - Qin, Junjie

AU - Vang, Søren

AU - Vilella, Albert J

AU - Ureta-Vidal, Abel

AU - Bolund, Lars

AU - Wang, Jun

AU - Durbin, Richard

PY - 2008

Y1 - 2008

N2 - 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.

AB - 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.

U2 - 10.1093/nar/gkm1005

DO - 10.1093/nar/gkm1005

M3 - Journal article

C2 - 18056084

SN - 0261-3166

VL - 36

SP - D735-D740

JO - Nucleic acids symposium series

JF - Nucleic acids symposium series

IS - Database issue

ER -

TreeFam: 2008 Update

Abstract

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