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Computational Molecular Evolution$
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Ziheng Yang

Print publication date: 2006

Print ISBN-13: 9780198567028

Published to Oxford Scholarship Online: April 2010

DOI: 10.1093/acprof:oso/9780198567028.001.0001

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Maximum likelihood methods

Maximum likelihood methods

Chapter:
(p.100) 4 Maximum likelihood methods
Source:
Computational Molecular Evolution
Author(s):

ZIHENG YANG

Publisher:
Oxford University Press
DOI:10.1093/acprof:oso/9780198567028.003.0004

This chapter discusses likelihood calculation for multiple sequences on a phylogenetic tree. As indicated at the end of Chapter 3, this is a natural extension to the parsimony method when we want to incorporate differences in branch lengths and in substitution rates between nucleotides. Likelihood calculation on a tree is also a natural extension to estimation of the distance between two sequences, discussed in Chapter 1. Exercises are provided at the end of the chapter.

Keywords:   likelihood calculation, phylogentic tree, maximum likelihood estimation, ancestral reconstruction

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