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Phylogenetic Trees From Sequences

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Problem Solving Handbook in Computational Biology and Bioinformatics

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Abstract

In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

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Author information

Authors and Affiliations

  1. Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, USA

    Paul Ryvkin

  2. Penn Center for Bioinformatics, Philadelphia, USA

    Li-San Wang

Authors
  1. Paul Ryvkin
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  2. Li-San Wang
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Correspondence to Paul Ryvkin .

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Editors and Affiliations

  1. Dept. Computer Science, Virginia Tech, Torgersen Hall 2050, Blacksburg, 24061-0106, Virgin Islands, USA

    Lenwood S. Heath

  2. Dept. Computer Science, Virginia Tech, Torgersen Hall 2050, Blacksburg, 24061-0106, Virgin Islands, USA

    Naren Ramakrishnan

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Ryvkin, P., Wang, LS. (2010). Phylogenetic Trees From Sequences. In: Heath, L., Ramakrishnan, N. (eds) Problem Solving Handbook in Computational Biology and Bioinformatics. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-09760-2_6

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  • DOI: https://doi.org/10.1007/978-0-387-09760-2_6

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