期刊
MOLECULAR ECOLOGY RESOURCES
卷 17, 期 6, 页码 1385-1392出版社
WILEY
DOI: 10.1111/1755-0998.12676
关键词
incongruence; multivariate analysis; package; software; tree distances; tree metric
资金
- Medical Research Council Centre for Outbreak Analysis and Modelling [MR/K010174/1]
- National Institute for Health Research-Health Protection Research Unit for Modelling Methodology [HPRU-2012-10080]
- Engineering and Physical Sciences Research Council (EPSRC) [EP/K026003/1]
- Engineering and Physical Sciences Research Council [EP/K026003/1] Funding Source: researchfish
- Medical Research Council [MR/K010174/1B] Funding Source: researchfish
- National Institute for Health Research [HPRU-2012-10080] Funding Source: researchfish
- EPSRC [EP/K026003/1] Funding Source: UKRI
The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low-dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group-specific consensus phylogenies. treespace also provides a user-friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results.
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