ArticlePeerJ2020
Iroki: automatic customization and visualization of phylogenetic trees.
Article in PeerJ, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
What it found
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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.
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Who cites it
75 citing papers in PubMed.
- Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut.Nature communications · 2021Trial
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- Monitoring viral evolution and epidemiological characteristics of SARS-CoV-2 during 2022-2023 using Integrated Genomic Surveillance.Communications medicine · 2026Article
- Single amino acid substitution in DNA Polymerase I dramatically alters infection dynamics of bacteriophage T7.bioRxiv : the preprint server for biology · 2026Article
- Uncovering superior alleles and genetic loci for yield-related traits in mungbean (Vigna radiata L. Wilczek) through a genome-wide association study.BMC plant biology · 2026Article
- Stability and age-specific patterns of rhinovirus circulation in children observed over 3 decades.The Journal of allergy and clinical immunology · 2026Article
- Knockout of nAChR subunits in spider mites and their phytoseiid predators confers spinosyn cross-resistance and reveals a conserved mode of action in mites.Insect biochemistry and molecular biology · 2026Article
- Comparative Genomics Reveals Unique Genetic Determinants of Biofilm Formation inInternational journal of molecular sciences · 2026Article
- Ribonucleotide reductases recapitulate biogeographic patterns within virioplankton according to ocean biogeochemistry.bioRxiv : the preprint server for biology · 2026Article
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- Outbreak of New Delhi metallo-β-lactamase carbapenemase-producing Pseudomonas aeruginosa infections in a Southern California hospital.American journal of infection control · 2025Article
- Dissecting the genetic and phenotypic basis of salinity tolerance in mungbean: insights from multi-stage phenotyping, GWAS and genomic prediction.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis.Molecular biology and evolution · 2025Article
- Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector.PLoS genetics · 2025Article
- Comparative Genomic Analysis ofMicroorganisms · 2025Article
- Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza.Virus evolution · 2025Article
- Fine-tuning protein language models unlocks the potential of underrepresented viral proteomes.PeerJ · 2025Article
- SoybeanViruses · 2024Article
- RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level.Genome biology · 2024Article
15 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
5 authors.
Funding
Abstract
Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki's utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki's source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
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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.