ArticleMolecular biology and evolution2020
Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 351 papers, 2 of them syntheses that pooled it.
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
351 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Meta-Analysis of the Gut Microbiome: An African American Representation.International journal of environmental research and public health · 2025Pooled it
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- Insights into goatpox virus and sheeppox virus genomes from pangenome graphs.Archives of virology · 2026Article
- Non-redundant cardiolipin synthase family proteins shape lipid composition and stress resilience inbioRxiv : the preprint server for biology · 2026Article
- Unravelling Complex Hybrid and Polyploid Evolutionary Relationships Using Phylogenetic Placement of Homologous Gene Copies from Target Enrichment Data.Systematic biology · 2026Article
- Mitogenomic Insights Into the Ancient Split and Cryptic Diversity of theEcology and evolution · 2026Article
- Distinct mechanisms of neutralization by antibodies targeting a conserved pneumovirus F epitope.bioRxiv : the preprint server for biology · 2026Article
- Identification of a candidate self-incompatibility locus in beet (Beta vulgaris).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
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- Whole-Genome Sequencing-Based Characterisation ofMicroorganisms · 2026Article
- Functional annotation of insulin-responsive genes in human adipocytes reveals PLCXD1 as a lipid storage regulator.Nature communications · 2026Article
- Weak but Repeated Patterns of Co-Introgression of Nuclear OXPHOS Genes and Mitochondrial DNA in Iberian Wall Lizards.Genome biology and evolution · 2026Article
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- Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa.PLoS pathogens · 2026Article
- Murbeckiella is dead, long live Oreophyton: origin and systematics of tribe Oreophytoneae (Brassicaceae).Annals of botany · 2026Article
- Lifestyles ofProceedings of the National Academy of Sciences of the United States of America · 2026Article
- A tale of two lineages: comparative biogeography across the Southern Cone of two South American Carex (Cyperaceae) groups.Annals of botany · 2026Article
- A global phylogenetic framework for Diospyros L. (Ebenaceae, Ericales): enhanced taxon and sample coverage through NGS, Sanger sequencing and herbariomics.Annals of botany · 2026Article
291 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors.
Funding
Abstract
Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.
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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.