Genome Rearrangement Phylogeny Using Weighbor

  • Li-San Wang 
Conference paper

DOI: 10.1007/3-540-45784-4_9

Part of the Lecture Notes in Computer Science book series (LNCS, volume 2452)
Cite this paper as:
Li-San W. (2002) Genome Rearrangement Phylogeny Using Weighbor. In: Guigó R., Gusfield D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg

Abstract

Evolution operates on whole genomes by operations that change the order and strandedness of genes within the genomes. This type of data presents new opportunities for discoveries about deep evolutionary rearrangement events. Several distance-based phylogenetic reconstruction methods have been proposed [12],[21],[19] that use neighbor joining (NJ) [16] with the expected breakpoint or inversion distances after k rearrangement events. In this paper we study the variance of the breakpoint and inversion distances. The result is combined with Weighbor [5], an improved version of NJ using the variance of true evolutionary distance estimators, to yield two new methods, Weighbor-IEBP and Weighbor-EDE. Experiments show the new methods have better accuracy than all previous distance-based methods, and are robust against model parameter misspecifications.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Li-San Wang 
    • 1
  1. 1.Department of Computer SciencesUniversity of TexasAustinUSA

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