ArticlePLoS biology2022
OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.
Article in PLoS biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 35 citations in OpenAlex.
- Coordinated P450-UGT detoxification contributes to furanocoumarin tolerance associated with host plant range divergence in Helicoverpa.PLoS biology · 2026Article
- Brachiopod genome unveils the evolution of BMP signalling in bilaterian body patterning.Nature communications · 2026Article
- Conservation of bilaterian genome structure is the exception, not the rule.Genome biology · 2025Article
- ClipKIT in the browser: fast online trimming of multiple sequence alignments for phylogenetics.Nucleic acids research · 2025Article
- Phylogenomics of the tetraploid Hawaiian lobeliads: Implications for their origin, dispersal history, and adaptive radiation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls.Nature plants · 2025Article
- Developmental correspondence of juvenile stages across the locust, harlequin ladybird, and diamondback moth.iScience · 2024Article
- Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians.Molecular biology and evolution · 2024Article
- Diverse signatures of convergent evolution in cactus-associated yeasts.PLoS biology · 2024Article
- A taxon-rich and genome-scale phylogeny of Opisthokonta.PLoS biology · 2024Article
- Host and venom evolution in parasitoid wasps: does independently adapting to the same host shape the evolution of the venom gland transcriptome?BMC biology · 2024Article
- Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair.PLoS genetics · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Comparative Population Transcriptomics Provide New Insight into the Evolutionary History and Adaptive Potential of World Ocean Krill.Molecular biology and evolution · 2023Article
- Diverse signatures of convergent evolution in cacti-associated yeasts.bioRxiv : the preprint server for biology · 2023Article
- Benchmarking gene set of gymnosperms for assessing genome and annotation completeness in BUSCO.Horticulture research · 2023Article
- CryptoCEN: A Co-Expression Network forbioRxiv : the preprint server for biology · 2023Article
- BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data.Genetics · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of selection, often rely on gene families of single-copy orthologs (SC-OGs). Large gene families with multiple homologs in 1 or more species-a phenomenon observed among several important families of genes such as transporters and transcription factors-are often ignored because identifying and retrieving SC-OGs nested within them is challenging. To address this issue and increase the number of markers used in molecular evolution studies, we developed OrthoSNAP, a software that uses a phylogenetic framework to simultaneously split gene families into SC-OGs and prune species-specific inparalogs. We term SC-OGs identified by OrthoSNAP as SNAP-OGs because they are identified using a splitting and pruning procedure analogous to snapping branches on a tree. From 415,129 orthologous groups of genes inferred across 7 eukaryotic phylogenomic datasets, we identified 9,821 SC-OGs; using OrthoSNAP on the remaining 405,308 orthologous groups of genes, we identified an additional 10,704 SNAP-OGs. Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar, even in complex datasets that contain a whole-genome duplication, complex patterns of duplication and loss, transcriptome data where each gene typically has multiple transcripts, and contentious branches in the tree of life. OrthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.