ArticleBioinformatics (Oxford, England)2014
kdetrees: Non-parametric estimation of phylogenetic tree distributions.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Pangenome-Wide Association Study in theInternational journal of molecular sciences · 2024Article
- Tukey's Depth for Object Data.Journal of the American Statistical Association · 2023Article
- The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genusFrontiers in plant science · 2022Article
- Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage.Evolutionary applications · 2021Article
- Riding the wave of genomics to investigate aquatic coliphage diversity and activity.Environmental microbiology · 2019Article
- GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the GenusFrontiers in microbiology · 2018Article
- The Genomic Basis of Intrinsic and Acquired Antibiotic Resistance in the GenusFrontiers in microbiology · 2018Article
- Reconstructing evolutionary trees in parallel for massive sequences.BMC systems biology · 2017Article
- Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees.Biometrika · 2017Article
- Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi.G3 (Bethesda, Md.) · 2017Article
- Reticulation, divergence, and the phylogeography-phylogenetics continuum.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Clustering Genes of Common Evolutionary History.Molecular biology and evolution · 2016Article
- Assessing parallel gene histories in viral genomes.BMC evolutionary biology · 2016Article
- Distances Between Extension Spaces of Phylogenetic Trees.IEEE transactions on computational biology and bioinformaticsArticle
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Authors and funding
5 authors.
Funding
Abstract
motivationAlthough the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well known that numerous other coexisting processes (e.g. horizontal gene transfers, gene duplication and subsequent neofunctionalization) will cause some genes to exhibit a history distinct from those of the majority of genes. Such 'outlying' gene trees are considered to be biologically interesting, and identifying these genes has become an important problem in phylogenetics.
resultsWe propose and implement kdetrees, a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. Our method compares favorably with a similar recently published method, featuring an improvement of one polynomial order of computational complexity (to quadratic in the number of trees analyzed), with simulation studies suggesting only a small penalty to classification accuracy. Application of kdetrees to a set of Apicomplexa genes identified several unreliable sequence alignments that had escaped previous detection, as well as a gene independently reported as a possible case of horizontal gene transfer. We also analyze a set of Epichloë genes, fungi symbiotic with grasses, successfully identifying a contrived instance of paralogy. AVAILABILITY AND IMPLEMENTATION: Our method for estimating tree distributions and identifying outlying trees is implemented as the R package kdetrees and is available for download from CRAN.
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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.