A new algorithm for reconstruction of phylogenetic tree

Authors:
ZhiHua Du;Zhen Ji
Affiliations:
ShenZhen Unvierstiy, Shenzhen, China;ShenZhen Unvierstiy, Shenzhen, China
Venue:
AIRS'08 Proceedings of the 4th Asia information retrieval conference on Information retrieval technology
Year:
2008

Citing 5
Cited 0

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Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees

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RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

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Abstract

The abstract should summarize the contents of the paper and should contain at least 70 and at most 150 words. It should be set in 9-point font size and should be inset 1.0 cm from the right and left margins. There should be two blank (10-point) lines before and after the abstract. This document is in the required format. In this paper, we present a new algorithm for reconstructing large phylogenetic tree. This algorithm is based on a family of Disk-Covering Methods (DCMs) which are divide-and-conquer techniques by dividing input dataset into smaller overlapping subset, constructing phylogenetic trees separately using some base methods and merging these subtrees into a single one. Provided the high memory efficiency of RAxML (which the program inherited from fastDNAml) compared to other programs and the good performance on largereal-world data it appears to be best-suited for use as the base method. The experiments clearly show that the proposed algorithm improves over stand-alone RAxML on all datasets, i.e. yields better likelihood values than RAxML in the same amount of time. This results serve as an argument for the choice of the proposed algorithm instead of stand-alone RAxML.