BUILDING VERY LARGE NEIGHBOUR-JOINING TREES

Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen

2010

Abstract

The neighbour-joining method by Saitou and Nei is a widely used method for phylogenetic reconstruction, made popular by a combination of computational efficiency and reasonable accuracy. With its cubic running time by Studier and Kepler, the method scales to hundreds of species, and while it is usually possible to infer phylogenies with thousands of species, tens or hundreds of thousands of species is infeasible. Recently we developed a simple branch and bound heuristic, RapidNJ, which significantly reduces the average running time. However, the O(n^2) space consumption of the RapidNJ method, and the NJ method in general, becomes a problem when inferring phylogenies with 10000+ taxa. In this paper we present two extentions of RapidNJ which reduce memory requirements and enable RapidNJ to infer very large phylogenetic trees efficiently. We also present an improved search heuristic for RapidNJ which improves RapidNJ’s performance on many data sets of all sizes.

Paper Citation

in Harvard Style

Simonsen M., Mailund T. and N. S. Pedersen C. (2010). BUILDING VERY LARGE NEIGHBOUR-JOINING TREES . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 26-32. DOI: 10.5220/0002715700260032

in Bibtex Style

@conference{bioinformatics10,
author={Martin Simonsen and Thomas Mailund and Christian N. S. Pedersen},
title={BUILDING VERY LARGE NEIGHBOUR-JOINING TREES},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={26-32},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002715700260032},
isbn={978-989-674-019-1},
}

in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - BUILDING VERY LARGE NEIGHBOUR-JOINING TREES
SN - 978-989-674-019-1
AU - Simonsen M.
AU - Mailund T.
AU - N. S. Pedersen C.
PY - 2010
SP - 26
EP - 32
DO - 10.5220/0002715700260032