Simple reconstruction of binary near-perfect phylogenetic trees

Srinath Sridhar*, Kedar Dhamdhere, Guy E. Blelloch, Eran Halperin, R. Ravi, Russell Schwartz

*Corresponding author for this work

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

4 Scopus citations


We consider the problem of reconstructing near-perfect phylogenetic trees using binary character states (referred to as BNPP). A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree, yielding an algorithm for binary character states that is computationally efficient but not robust to imperfections in real data. A near-perfect phylogeny relaxes the perfect phylogeny assumption by allowing at most a constant number q of additional mutations. In this paper, we develop an algorithm for constructing optimal phylogenies and provide empirical evidence of its performance. The algorithm runs in time O((72κ)qnm + nm2) where n is the number of taxa, m is the number of characters and κ is the number of characters that share four gametes with some other character. This is fixed parameter tractable when q and κ are constants and significantly improves on the previous asymptotic bounds by reducing the exponent to q. Furthermore, the complexity of the previous work makes it impractical and in fact no known implementation of it exists. We implement our algorithm and demonstrate it on a selection of real data sets, showing that it substantially outperforms its worstcase bounds and yields far superior results to a commonly used heuristic method in at least one case. Our results therefore describe the first practical phylogenetic tree reconstruction algorithm that finds guaranteed optimal solutions while being easily implemented and computationally feasible for data sets of biologically meaningful size and complexity.

Original languageEnglish
Title of host publicationComputational Science - ICCS 2006
Subtitle of host publication6th International Conference, Proceedings
PublisherSpringer Verlag
Number of pages8
ISBN (Print)3540343814, 9783540343813
StatePublished - 2006
Externally publishedYes
EventICCS 2006: 6th International Conference on Computational Science - Reading, United Kingdom
Duration: 28 May 200631 May 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3992 LNCS - II
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


ConferenceICCS 2006: 6th International Conference on Computational Science
Country/TerritoryUnited Kingdom


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