ArticleMolecular biology and evolution2021
Orthology Clusters from Gene Trees with Possvm.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- BAT: an integrated pipeline for gene tree construction, annotation, and functional inference.bioRxiv : the preprint server for biology · 2026Article
- Functional characterization of specialized immune cells in a cnidarian reveals an ancestral antiviral program.Nature communications · 2026Article
- Hyper-specialized primates possess a reduced suite of xenobiotic-metabolizing cytochrome P450 genes.Molecular phylogenetics and evolution · 2026Article
- eggNOG v7: phylogeny-based orthology predictions and functional annotations.Nucleic acids research · 2026Article
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- Evolutionary Dynamics of Glycoside Hydrolase Family 1 Provide Insights into Insect-Plant Interactions in Lepidoptera.Insects · 2025Article
- An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm.Nature communications · 2024Article
- Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids.Nature communications · 2024Article
- Quantifying microbial guilds.ISME communications · 2024Article
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- Balanophora genomes display massively convergent evolution with other extreme holoparasites and provide novel insights into parasite-host interactions.Nature plants · 2023Article
- Gene losses, parallel evolution and heightened expression confer adaptations to dedicated cleaning behaviour.BMC biology · 2023Article
- Cell type diversity in a developing octopus brain.Nature communications · 2022Article
- A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution.Nature ecology & evolution · 2022Article
- Advancing phylogenomics in Amaranthaceae sensu stricto: Development and application of a new nuclear target enrichment bait set.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL [Markov clustering algorithm]) is a tool that automates the process of identifying clusters of orthologous genes from precomputed phylogenetic trees and classifying gene families. It identifies orthology relationships between genes using the species overlap algorithm to infer taxonomic information from the gene tree topology, and then uses the MCL to identify orthology clusters and provide annotated gene families. Our benchmarking shows that this approach, when provided with accurate phylogenies, is able to identify manually curated orthogroups with very high precision and recall. Overall, Possvm automates the routine process of gene tree inspection and annotation in a highly interpretable manner, and provides reusable outputs and phylogeny-aware gene annotations that can be used to inform comparative genomics and gene family evolution analyses.
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Registered trials
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