EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
Open accessAbstract
We have developed a comprehensive gene orientated phylogenetic resource, EnsemblCompara GeneTrees, based on a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. We developed two novel non-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam shows the best performance in our hands. We also compared this phylogenetic approach to clustering approaches for ortholog prediction, showing a large increase in coverage using the phylogenetic approach. All data are made available in a number of formats and will be kept up to date with the Ensembl project.
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TOGA detected 97.6%, 98.9% and 96.5% of the orthologs provided by Ensembl for human-rat, human-cow, and human-elephant comparisons, respectively.
“Using orthologs between human and three representative mammals (rat, cow, elephant), TOGA detected 97.6%, 98.9% and 96.5% of the orthologs provided by Ensembl (Fig. 2A, Table S5), showing a good agreement.”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [14]
The 'Overlap of ortholog sets' section describes EnsemblCompara ortholog predictions, supporting the identification of Ensembl as an ortholog source. It does not report a TOGA comparison or the 97.6%, 98.9%, and 96.5% detection rates; those results are not supported by this paper. (LLM, conf=0.88)
Experimental — accuracy not yet measuredOrthologous chains tend to cover several genes located in a conserved order, resulting in higher synteny values, which can help distinguish orthologs from paralogs.
“Orthologous chains tend to cover several genes located in a conserved order, resulting in higher synteny values, which can help to distinguish orthologs from paralogs (14, 41–43).”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [14]
The Gene synteny metric section (page unavailable) says that ordered, flanking orthologous genes indicate conserved gene order, and the Comparison using the synteny metric section uses that measure to assess prediction specificity. The paper does not describe orthologous chains or show that they have higher synteny values than paralogous chains; it also says synteny was not used directly to build its trees. (LLM, conf=0.82)
Experimental — accuracy not yet measuredGene tree-based methods determine whether the evolutionary lineages of two genes coalesce in a speciation or a duplication node.
“Gene tree-based methods determine whether the evolutionary lineages of two genes coalesce in a speciation or a duplication node (12–14).”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [14]
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- Authors
- Vilella, A. J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R., & Birney, E.
- Affiliations
- European Bioinformatics Institute (GB)
- Wellcome Sanger Institute (GB)
- ORCID
- Birney, Ewan
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-11-24
- Volume
- 19
- Issue
- 2
- Pages
- 327-335
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2652215
- OpenAlex
- W7098320409
- Cited by
- 1,238
- References
- 5
- Citations by year
- 2026: 36 · 2025: 59 · 2024: 65 · 2023: 48 · 2022: 61 · 2021: 81 · 2020: 78 · 2019: 61 · 2018: 75 · 2017: 100 · 2016: 81 · 2015: 97 · 2014: 94 · 2013: 104 · 2012: 65
- Type
- posted content
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Genome Research (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- gene trees, gene family evolution, ortholog prediction, multiple sequence alignment, gene clustering, vertebrate genomes
- MeSH terms
- Algorithms, Animals, Multigene Family, Humans, Models, Biological, Phylogeny, Software, Vertebrates, Sequence Homology, Computational Biology, Gene Duplication, Synteny
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