ArticleG3 (Bethesda, Md.)2021
orthofisher: a broadly applicable tool for automated gene identification and retrieval.
Article in G3 (Bethesda, Md.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 50 citations in OpenAlex.
- Regions of low gene expression promote maintenance and adaptation of horizontally acquired genes in yeasts.Communications biology · 2026Article
- ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.Molecular ecology resources · 2026Article
- Pseudomonas eutrophicaquae sp. nov., a novel xenobiotic-degrading non-motile bacterium, containing Q-8 ubiquinone, isolated from an aquatic ecosystem in Jimo District, China.Antonie van Leeuwenhoek · 2026Article
- FrlP, an ABC type I importer component ofJournal of bacteriology · 2025Article
- Stable Hypermutators Revealed by the Genomic Landscape of Genes Involved in Genome Stability Among Yeast Species.Molecular biology and evolution · 2025Article
- Small pangenome ofmBio · 2025Article
- Convergent reductive evolution in bee-associated lactic acid bacteria.Applied and environmental microbiology · 2024Article
- A taxon-rich and genome-scale phylogeny of Opisthokonta.PLoS biology · 2024Article
- Convergent reductive evolution in bee-associated lactic acid bacteria.bioRxiv : the preprint server for biology · 2024Article
- Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information.Journal of integrative bioinformatics · 2024Article
- Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage.BMC biology · 2024Article
- Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts.Science (New York, N.Y.) · 2024Article
- Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae.BMC biology · 2024Article
- Phylogenomics reveals extensive misidentification of fungal strains from the genusMicrobiology spectrum · 2024Article
- Review
- Genomic and ecological factors shaping specialism and generalism across an entire subphylum.bioRxiv : the preprint server for biology · 2023Article
- The evolution of antimicrobial peptides in Chiroptera.Frontiers in immunology · 2023Article
- OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.PLoS biology · 2022Article
- BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data.Genetics · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Identification and retrieval of genes of interest from genomic data are an essential step for many bioinformatic applications. We present orthofisher, a command-line tool for automated identification and retrieval of genes with high sequence similarity to a query profile Hidden Markov Model sequence alignment across a set of proteomes. Performance assessment of orthofisher revealed high accuracy and precision during single-copy orthologous gene identification. orthofisher may be useful for assessing gene annotation quality, identifying single-copy orthologous genes for phylogenomic analyses, estimating gene copy number, and other evolutionary analyses that rely on identification and retrieval of homologous genes from genomic data. orthofisher comes complete with comprehensive documentation (https://jlsteenwyk.com/orthofisher/), is freely available under the MIT license, and is available for download from GitHub (https://github.com/JLSteenwyk/orthofisher), PyPi (https://pypi.org/project/orthofisher/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/orthofisher).
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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.