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    Comparison of mode estimation methods and application in molecular clock analysis

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    Comparison of mode estimation ...
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    Genre
    Journal Article
    Date
    2003-07-31
    Author
    Hedges, SB
    Shah, P
    Subject
    Ascomycota
    Basidiomycota
    Biological Clocks
    Bryophyta
    Chlorophyta
    Computational Biology
    Computer Simulation
    Evolution, Molecular
    Models, Statistical
    Normal Distribution
    Plants
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    Permanent link to this record
    http://hdl.handle.net/20.500.12613/5663
    
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    DOI
    10.1186/1471-2105-4-31
    Abstract
    Background: Distributions of time estimates in molecular clock studies are sometimes skewed or contain outliers. In those cases, the mode is a better estimator of the overall time of divergence than the mean or median. However, different methods are available for estimating the mode. We compared these methods in simulations to determine their strengths and weaknesses and further assessed their performance when applied to real data sets from a molecular clock study. Results: We found that the half-range mode and robust parametric mode methods have a lower bias than other mode methods under a diversity of conditions. However, the half-range mode suffers from a relatively high variance and the robust parametric mode is more susceptible to bias by outliers. We determined that bootstrapping reduces the variance of both mode estimators. Application of the different methods to real data sets yielded results that were concordant with the simulations. Conclusion: Because the half-range mode is a simple and fast method, and produced less bias overall in our simulations, we recommend the bootstrapped version of it as a general-purpose mode estimator and suggest a bootstrap method for obtaining the standard error and 95% confidence interval of the mode. © 2003 Hedges and Shah; licensee BioMed Central Ltd.
    Citation to related work
    Springer Science and Business Media LLC
    Has part
    BMC Bioinformatics
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    For Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.34944/dspace/5645
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