Literature DB >> 16969941

A geometric approach to tree shape statistics.

Frederick A Matsen1.   

Abstract

This article presents a new way to quantify the descriptive ability of tree shape statistics. Where before, tree shape statistics were chosen by their ability to distinguish between macroevolutionary models, the resolution presented in this paper quantifies the ability of a statistic to differentiate between similar and different trees. This is termed the geometric approach to differentiate it from the model-based approach previously explored. A distinct advantage of this perspective is that it allows evaluation of multiple tree shape statistics describing different aspects of tree shape. After developing the methodology, it is applied here to make specific recommendations for a suite of three statistics that may prove useful in applications. The article ends with an application of the statistics to clarify the impact of taxa omission on tree shape.

Mesh:

Year:  2006        PMID: 16969941     DOI: 10.1080/10635150600889617

Source DB:  PubMed          Journal:  Syst Biol        ISSN: 1063-5157            Impact factor:   15.683


  15 in total

1.  Stochastic models for phylogenetic trees on higher-order taxa.

Authors:  David Aldous; Maxim Krikun; Lea Popovic
Journal:  J Math Biol       Date:  2007-10-02       Impact factor: 2.259

2.  A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition.

Authors:  Niema Moshiri; Siavash Mirarab
Journal:  Syst Biol       Date:  2018-05-01       Impact factor: 15.683

3.  Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree.

Authors:  Zongfeng Yang; Junrui Li; Thomas Wiehe; Haipeng Li
Journal:  Genetics       Date:  2017-12-07       Impact factor: 4.562

4.  A Metric on Phylogenetic Tree Shapes.

Authors:  C Colijn; G Plazzotta
Journal:  Syst Biol       Date:  2018-01-01       Impact factor: 15.683

5.  Predicting the short-term success of human influenza virus variants with machine learning.

Authors:  Maryam Hayati; Priscila Biller; Caroline Colijn
Journal:  Proc Biol Sci       Date:  2020-04-08       Impact factor: 5.349

6.  Phylogenetic properties of RNA viruses.

Authors:  Simone Pompei; Vittorio Loreto; Francesca Tria
Journal:  PLoS One       Date:  2012-09-20       Impact factor: 3.240

7.  Coverage statistics for sequence census methods.

Authors:  Steven N Evans; Valerie Hower; Lior Pachter
Journal:  BMC Bioinformatics       Date:  2010-08-18       Impact factor: 3.169

8.  Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials.

Authors:  Frederick A Matsen; Steven N Evans
Journal:  Algorithms Mol Biol       Date:  2012-05-21       Impact factor: 1.405

9.  Quantifying MCMC exploration of phylogenetic tree space.

Authors:  Chris Whidden; Frederick A Matsen
Journal:  Syst Biol       Date:  2015-01-27       Impact factor: 15.683

10.  Universal artifacts affect the branching of phylogenetic trees, not universal scaling laws.

Authors:  Cristian R Altaba
Journal:  PLoS One       Date:  2009-02-26       Impact factor: 3.240

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