Deferred path heuristic for phylogenetic trees revisited

B. K. Nielsen, S. Lindgren, S. Winter, Martin Tvede Zachariasen

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

Abstract

We reexamine the deferred path heuristic originally developed by Schwikowski and Vingron in the late 1990s. Given a set of sequences, e.g. DNA, this heuristic simultaneously finds a multiple alignment and a phylogenetic tree. We give a unified description of the heuristic where such intermediate constructs as fork alignment graphs are made obsolete. Based on this description an efficient implementation is straightforward. We discuss two improvements of which one is intended to provide better quality solutions and one is intended to provide a substantial speed-up. This is confirmed by experiments on several real-life problem instances.
Original languageEnglish
Title of host publicationProceedings Of CompBioNets05
Subtitle of host publicationAlgorithms and Computional Methods for Biochemical and Evolutionary Networks
PublisherKing's College Publications
Pages75-92
Number of pages18
Publication statusPublished - 2005
EventAlgorithms and Computional Methods for Biochemical and Evolutionary Networks - Lyon, France
Duration: 5 Dec 20057 Dec 2005
Conference number: 2

Conference

ConferenceAlgorithms and Computional Methods for Biochemical and Evolutionary Networks
Country/TerritoryFrance
CityLyon
Period5/12/057/12/05

Keywords

  • computional biology
  • Evolutionary trees

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