ArticleMicrobial genomics2019
HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny.
Article in Microbial genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments.Molecular biology and evolution · 2026Article
- Tracing 2500 years of human betaherpesvirus 6A and 6B diversity through ancient DNA.Science advances · 2026Article
- Triazole Resistance and Misidentification of Aspergillus tubingensis in Southern California.JAMA network open · 2025Article
- The araneopathogenic genusFungal systematics and evolution · 2025Article
- Hotspots of genetic change in Yersinia pestis.Nature communications · 2025Article
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- Average Nucleotide Identity basedbioRxiv : the preprint server for biology · 2024Article
- Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach.Nature communications · 2024Article
- Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic.Virus evolution · 2024Article
- Quantitative measurement of antibiotic resistance inResearch square · 2023Article
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- Evolution and epidemic success of Mycobacterium tuberculosis in eastern China: evidence from a prospective study.BMC genomics · 2023Article
- White-tailed deer (Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genomic changes underpinning the emergence of a successfulFrontiers in microbiology · 2023Article
- Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches.mSystems · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A homoplasy is a nucleotide identity resulting from a process other than inheritance from a common ancestor. Importantly, by distorting the ancestral relationships between nucleotide sequences, homoplasies can change the structure of the phylogeny. Homoplasies can emerge naturally, especially under high selection pressures and/or high mutation rates, or be created during the generation and processing of sequencing data. Identification of homoplasies is critical, both to understand their influence on the analyses of phylogenetic data and to allow an investigation into how they arose. Here we present HomoplasyFinder, a java application that can be used as a stand-a-lone tool or within the statistical programming environment R. Within R and Java, HomoplasyFinder is shown to be able to automatically, and quickly, identify any homoplasies present in simulated and real phylogenetic data. HomoplasyFinder can easily be incorporated into existing analysis pipelines, either within or outside of R, allowing the user to quickly identify homoplasies to inform downstream analyses and interpretation.
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