ArticleGenome biology2022
SHOOT: phylogenetic gene search and ortholog inference.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed.
- Iterative and data-driven ortholog mining enables reliable discovery of stereoselective ketoreductases.Nature communications · 2026Article
- OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability.Nature methods · 2026Article
- The Effects of Rapid Mitochondrial Gene Loss on Organellar Proteomes.Genome biology and evolution · 2026Article
- DupyliCate: mining, classifying, and characterizing gene duplications.Scientific reports · 2026Article
- Article
- Molecular insights into electroreceptor ribbon synapses from differential gene expression in sturgeon lateral line organs.Journal of anatomy · 2026Article
- Optimizing the hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) protocol forbioRxiv : the preprint server for biology · 2026Article
- PharaohFUN: phylogenomic analysis for plant protein history and function elucidation.Molecular biology and evolution · 2026Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees.Journal of molecular evolution · 2025Article
- Temporal regulation of gene expression during auxin-triggered crown root formation in barley: an integrated approach.Plant & cell physiology · 2025Article
- A stress-induced paralog of Lhcb4 controls the photosystem II functional architecture in Arabidopsis thaliana.Nature communications · 2025Article
- CRISPR/Cas9 Knockout of Shell Matrix Protein 1 in the Slipper-Snail Crepidula atrasolea.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Article
- Novel perspectives on plastome evolution in Onagraceae.AoB PLANTS · 2025Article
- Shining light on Arabidopsis regulatory networks integrating nitrogen use and photosynthesis.The Plant journal : for cell and molecular biology · 2025Article
- A SecA-associated protease modulates the extent of surface display of staphylococcal protein A.Journal of bacteriology · 2025Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs.Bioinformatics (Oxford, England) · 2024Article
- Evolution and related pathogenic genes of Pseudodiploöspora longispora on Morchella based on genomic characterization and comparative genomic analysis.Scientific reports · 2024Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees and returns a tree with the query sequence correctly placed within it. We show that SHOOT performs this analysis with comparable speed to a BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional tree inference, and it can identify orthologs with high accuracy. In summary, SHOOT is a fast and accurate tool for phylogenetic analyses of novel query sequences. It is available online at www.shoot.bio .
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.