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GeneTrees specifications


Unique identifier OMICS_21018
Name GeneTrees
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No


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Publication for GeneTrees

GeneTrees citations


The Evolution and Functional Diversification of the Deubiquitinating Enzyme Superfamily

Genome Biol Evol
PMCID: 5381560
PMID: 28177072
DOI: 10.1093/gbe/evx020

[…] roup of animals where the new paralog is present (whereas verifying its absence in the syntenic region of more earlier diverging animals). DUBs that are predicted to be paralogs by the EnsemblCompara GeneTrees pipeline (), including ancestral DUBs, are grouped in . Paralogous pairs within these groups were inferred by reciprocal best BLAST (RBB) of new paralogs to determine their most likely ances […]


Lipid droplet biology and evolution illuminated by the characterization of a novel perilipin in teleost fish

PMCID: 5342826
PMID: 28244868
DOI: 10.7554/eLife.21771.025
call_split See protocol

[…] Phylogenetic analyses used EnsemblCompara GeneTrees (; ). This method starts with data in Ensembl genomes, and uses the longest protein translation for each gene, identifies the Best Reciprocal BlastP Hit, clusters data into gene families, al […]


The spotted gar genome illuminates vertebrate evolution and facilitates human to teleost comparisons

Nat Genet
PMCID: 4817229
PMID: 26950095
DOI: 10.1038/ng.3526

[…] Curated lists of TGD ohnologs and TGD singletons of zebrafish and medaka and their gar (co-)orthologs were generated by integrating phylogenetic information from EnsemblCompara GeneTrees (Ensembl74) and conserved synteny data from the Synteny Database (). For all three species, RNA-seq reads from the PhyloFish transcriptomes (,) were mapped against the longest Ensembl refere […]


Inferring Orthologs: Open Questions and Perspectives

PMCID: 4778853
PMID: 26966373
DOI: 10.4137/GEI.S37925

[…] didate gene families determined by similarity and then rely on merging gene and species phylogeny to determine the subset of orthologs: Orthostrapper, RIO, PhIGs, PhyOP, TreeFam, LOFT, EnsemblCompara GeneTrees based on TreeBeST method, SYNERGY, and PHOG. COCO-CL is based on a hierarchical clustering algorithm of correlated genes guided by phylogenetic relationships. Species phylogeny was originall […]


Ensembl comparative genomics resources

PMCID: 4761110
PMID: 26896847
DOI: 10.1093/database/bav096

[…] GeneTrees are built with all protein-coding genes in Ensembl, as well as three non-chordate model species, Caernobditis elegans, Drosophila melanogaster and Saccharomyces cereviciae, using our previou […]


Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

BMC Genomics
PMCID: 4603753
PMID: 26450506
DOI: 10.1186/1471-2164-16-S10-S1

[…] re, ASTRAL and ASTRAL-2 are statistically consistent under the bounded HGT models of [].We ran ASTRAL-2 version 4.7.6 on the simulated data using the following command: java -jar astral.4.7.6.jar -i <genetrees> -o where is a file containing the gene trees in newick format, and is the output.For the biological data, we used ASTRAL-2 with multi-locus bootstrapp […]


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GeneTrees institution(s)
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
GeneTrees funding source(s)
Supported in part by NSF grant 0114866, DOD contract W911SR-04-C-0045 and the Virginia Bioinformatics Institute.

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