TreeFam


24194607	TreeFam v9: a new website, more species and orthology-on-the-fly. [PMID: 24194607] Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A. Abstract TreeFam (http://www.treefam.org) is a database of phylogenetic trees inferred from animal genomes. For every TreeFam family we provide homology predictions together with the evolutionary history of the genes. Here we describe an update of the TreeFam database. The TreeFam project was resurrected in 2012 and has seen two releases since. The latest release (TreeFam 9) was made available in March 2013. It has orthology predictions and gene trees for 109 species in 15,736 families covering ?2.2 million sequences. With release 9 we made modifications to our production pipeline and redesigned our website with improved gene tree visualizations and Wikipedia integration. Furthermore, we now provide an HMM-based sequence search that places a user-provided protein sequence into a TreeFam gene tree and provides quick orthology prediction. The tool uses Mafft and RAxML for the fast insertion into a reference alignment and tree, respectively. Besides the aforementioned technical improvements, we present a new approach to visualize gene trees and alternative displays that focuses on showing homology information from a species tree point of view. From release 9 onwards, TreeFam is now hosted at the EBI. Nucleic Acids Res. 2014:42(Database issue) \| 92 Citations (from Europe PMC, 2025-03-22)
18056084	TreeFam: 2008 Update. [PMID: 18056084] Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, Wang J, Durbin R. 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. Nucleic Acids Res. 2008:36(Database issue) \| 227 Citations (from Europe PMC, 2025-03-22)
16381935	TreeFam: a curated database of phylogenetic trees of animal gene families. [PMID: 16381935] Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Wang J, Durbin R. Abstract TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; approximately 40-85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at http://www.treefam.org and http://treefam.genomics.org.cn. Nucleic Acids Res. 2006:34(Database issue) \| 335 Citations (from Europe PMC, 2025-03-22)

TreeFam v9: a new website, more species and orthology-on-the-fly. [PMID: 24194607]

Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.

TreeFam (http://www.treefam.org) is a database of phylogenetic trees inferred from animal genomes. For every TreeFam family we provide homology predictions together with the evolutionary history of the genes. Here we describe an update of the TreeFam database. The TreeFam project was resurrected in 2012 and has seen two releases since. The latest release (TreeFam 9) was made available in March 2013. It has orthology predictions and gene trees for 109 species in 15,736 families covering ?2.2 million sequences. With release 9 we made modifications to our production pipeline and redesigned our website with improved gene tree visualizations and Wikipedia integration. Furthermore, we now provide an HMM-based sequence search that places a user-provided protein sequence into a TreeFam gene tree and provides quick orthology prediction. The tool uses Mafft and RAxML for the fast insertion into a reference alignment and tree, respectively. Besides the aforementioned technical improvements, we present a new approach to visualize gene trees and alternative displays that focuses on showing homology information from a species tree point of view. From release 9 onwards, TreeFam is now hosted at the EBI.

Nucleic Acids Res. 2014:42(Database issue) | 92 Citations (from Europe PMC, 2025-03-22)

TreeFam: 2008 Update. [PMID: 18056084]

Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, Wang J, Durbin R.

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.

Nucleic Acids Res. 2008:36(Database issue) | 227 Citations (from Europe PMC, 2025-03-22)

TreeFam: a curated database of phylogenetic trees of animal gene families. [PMID: 16381935]

Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Wang J, Durbin R.

Abstract

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; approximately 40-85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at http://www.treefam.org and http://treefam.genomics.org.cn.

Nucleic Acids Res. 2006:34(Database issue) | 335 Citations (from Europe PMC, 2025-03-22)

URL:	http://www.treefam.org/
Full name:	database of phylogenetic trees
Description:	TreeFam is a database of phylogenetic trees inferred from animal genomes.
Year founded:	2006
Last update:	2013-3
Version:
Accessibility:	Accessible
Country/Region:	United Kingdom

Data type:	DNA
Data object:	Animal
Database category:	Phylogeny and homology
Major species:	Homo sapiens Saccharomyces cerevisiae
Keywords:	evolution orthology/parology predictions phylogenetic trees

University/Institution:	Wellcome Sanger Institute
Address:	Wellcome Trust Sanger Institute,Wellcome Trust Genome Campus,Hinxton,Cambridgeshire CB10 1SA,UK
City:	Cambridgeshire
Province/State:
Country/Region:	United Kingdom
Contact name (PI/Team):	Fabian Schreiber
Contact email (PI/Helpdesk):	fs@ebi.ac.uk

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