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Parsimony, Phylogeny, and Genomics$
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Victor A. Albert

Print publication date: 2006

Print ISBN-13: 9780199297306

Published to Oxford Scholarship Online: September 2007

DOI: 10.1093/acprof:oso/9780199297306.001.0001

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The limits of conventional cladistic analysis

The limits of conventional cladistic analysis

(p.118) (p.119) Chapter 7 The limits of conventional cladistic analysis
Parsimony, Phylogeny, and Genomics

Jerrold I. Davis

Kevin C. Nixon

Damon P. Little

Oxford University Press

Software for cladistic analysis has been widely available for more than twenty years, and a series of advances made during this time have facilitated the analysis of matrices of ever-increasing size. This chapter provides an overview of the development of parsimony methods for cladistic analysis, describes strategies that have allowed large data matrices to be analysed by conventional methods, and in doing so, demonstrates that data sets historically considered intracable could in fact have been readily approached using then-available hardware and software. Preliminary analyses, even when unsuccessful at discovering most-parsimonious trees, can be used to identify appropriate software settings for use during thorough analyses. A useful indicator of the settings that yield the most efficient searches is the excess branch swapping ratio, which is the ratio between the number of tree rearrangements conducted during a particular phase of branch swapping in which shorter trees are being discovered, and the minimum possible number of rearrangements during this phase. It is concluded that two-stage search strategies, with intensive branch swapping conducted on a small percentage of the most optimal sets of trees obtained by a large number of relatively short searches, are more efficient than one-stage searches.

Keywords:   parsimony methods, large data sets, excess branch swapping ration, rearrangements, two-stage searches, one-stage searches

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