The worst case complexity of maximum parsimony

Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations

Abstract

One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We re-examine the classical Maximum Parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze theworst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards [5], the approach of Hendy and Penny [12], and a new agglomerative, "bottomup" approach we present in this paper. We show that the second and third approaches are faster than the first by a factor of and Θ(n), respectively.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings
PublisherSpringer Verlag
Pages79-88
Number of pages10
ISBN (Print)9783319075655
DOIs
StatePublished - 1 Jan 2014
Event25th Annual Symposium on Combinatorial Pattern Matching, CPM 2014 - Moscow, Russian Federation
Duration: 16 Jun 201418 Jun 2014

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8486 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference25th Annual Symposium on Combinatorial Pattern Matching, CPM 2014
Country/TerritoryRussian Federation
CityMoscow
Period16/06/1418/06/14

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

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