ArticleBMC bioinformatics2017
A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history.
Article in BMC bioinformatics, 2017. 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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19 citing papers in PubMed.
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- CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.PeerJ. Computer science · 2025Article
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- Evaluation of canine raw food products for the presence of extended-spectrum beta-lactamase- and carbapenemase-producing bacteria of the order Enterobacterales.American journal of veterinary research · 2022Article
- Salmonella enterica Serovar Typhimurium Isolates from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type.Applied and environmental microbiology · 2022Article
- Characterization of 2Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2022Article
- A case report ofAccess microbiology · 2022Article
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- A Multidrug-ResistantMicrobial drug resistance (Larchmont, N.Y.) · 2021Article
- Determination of Genomic Epidemiology of Historical Clostridium perfringens Outbreaks in New York State by Use of Two Web-Based Platforms: National Center for Biotechnology Information Pathogen Detection and FDA GalaxyTrakr.Journal of clinical microbiology · 2021Article
- Selection-Driven Gene Inactivation in Salmonella.Genome biology and evolution · 2020Article
- Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance.Journal of clinical microbiology · 2019Review
- Methylation-Induced Hypermutation in Natural Populations of Bacteria.Journal of bacteriology · 2018Article
- Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis.Clinical microbiology reviews · 2017Review
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1 author.
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Abstract
backgroundMaximum compatibility is a method of phylogenetic reconstruction that is seldom applied to molecular sequences. It may be ideal for certain applications, such as reconstructing phylogenies of closely-related bacteria on the basis of whole-genome sequencing.
resultsHere I present an algorithm that rapidly computes phylogenies according to a compatibility criterion. Although based on solutions to the maximum clique problem, this algorithm deals properly with ambiguities in the data. The algorithm is applied to bacterial data sets containing up to nearly 2000 genomes with several thousand variable nucleotide sites. Run times are several seconds or less. Computational experiments show that maximum compatibility is less sensitive than maximum parsimony to the inclusion of nucleotide data that, though derived from actual sequence reads, has been identified as likely to be misleading.
conclusionsMaximum compatibility is a useful tool for certain phylogenetic problems, such as inferring the relationships among closely-related bacteria from whole-genome sequence data. The algorithm presented here rapidly solves fairly large problems of this type, and provides robustness against misleading characters than can pollute large-scale sequencing data.
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