Journal of applied mathematics & informatics
- Volume 25 Issue 1_2
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- Pages.455-470
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- 2007
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- 2734-1194(pISSN)
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- 2234-8417(eISSN)
ANALYSIS OF NEIGHBOR-JOINING BASED ON BOX MODEL
- Cho, Jin-Hwan (Department of Mathematics, The University of Suwon) ;
- Joe, Do-Sang (Deparment of Mathematics Education, Konkuk University) ;
- Kim, Young-Rock (Graduate School of Education, Hankuk University of Foreign Studies)
- Published : 2007.09.30
Abstract
In phylogenetic tree construction the neighbor-joining algorithm is the most well known method which constructs a trivalent tree from a pairwise distance data measured by DNA sequences. The core part of the algorithm is its cherry picking criterion based on the tree structure of each quartet. We give a generalized version of the criterion based on the exact box model of quartets, known as the tight span of a metric. We also show by experiment why neighbor-joining and the quartet consistency count method give similar performance.
Keywords
- Neighbor-joining;
- phylogenetic tree;
- tight span;
- quartet consistency;
- sequence generation;
- tree construction algorithm