TreeFam: a curated database of phylogenetic trees of animal gene families

By Heng Li, Avril Coghlan, Jue Ruan, L. Coin, Jean-Karim Hériché, Lara Osmotherly, Ruiqiang Li, Tao Liu, Zhang Zhang, Lars Bolund and 5 more. Nucleic Acids Res., 2005

506 citations recorded by the source corpus.

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; ∼40–85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at and .

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/16071555ad3dcc970b3fcfac598d308e882d3e9d

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Citations in the corpus

eggNOG: automated construction and annotation of orthologous groups of genes (2007, methodology): “Numerous methods have been developed to derive orthologs and orthologous groups, ranging from the simple reciprocal-best-hit approach, via InParanoid (5), MultiParanoid (6), identiﬁcation best-hit triangles (2,7,8) and clustering-based approaches (9), to tree-based meth-ods (10–13).”
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy (2015, methodology): “BLAST [14] is the most widely used method to identify and measure similarity between sequences and thus it underpins the majority of orthologue identification methods [9, 13, 21–23].”
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics (2014, methodology): “A number of orthology inference methods have been applied to phylogenomic analyses based on transcriptomes and low-coverage genomes, such as orthoMCL (Li et al. 2003), Hcluster_sg (as part of TreeFam; Li et al. 2006), SCaFoS (Roure et al. 2007), HaMStR (Ebersberger et al. 2009), and OrthoSelect (Sch”
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix (2009, methodology): “Finally, for Web sites that support interactive use of phylogenetic trees, it is desirable to compute trees for all the genes beforehand (Li et al. 2006; http://www.treefam.org/; http://www.microbesonline.org/).”
An integrative approach to ortholog prediction for disease-focused and other functional studies (2011, background): “Based on published reviews and comparative studies evaluating different tools, we selected nine tools that provide a reasonable balance of specificity and sensitivity [7-12,15,16,54-59].”
The yak genome and adaptation to life at high altitude (2012, methodology): “…6 mammalian species ( Canis familiaris , Homo sapiens , Mus musculus , B. taurus , Equus caballus and Monodelphis domestica ) downloaded from Ensembl (release 56; see URLs) were used in addition to yak genes to define gene families that descended from a single gene in the last common ancestor 20 .”
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes (2013, methodology): “In detail, we start with all sequence paralog and ortholog gene relations within each TreeFam [22] gene family.”
TreeFam: 2008 Update (2007, methodology): “Seventeen new species have been added since TreeFam v1 (4).”
The human phylome (2007, methodology): “Most remarkably, the Ensembl database now includes phylogenetic trees [12], and the TreeFam [13] and HOVERGEN [14] databases provide automatically derived and curated phylogenies of animal gene families.”
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. (2009, methodology): “In Table 1 we show that the concordance between our automated prediction set and the manually curated TreeFam data set is very high.”
Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum (2011, methodology): “uk/interpro/) in combination with the Treefam methodology that defines a protein family as a group of genes descended from a common ancestor [121].”