A fast neighbor joining method

Genetics and Molecular Research : GMR
J F Li

Abstract

With the rapid development of sequencing technologies, an increasing number of sequences are available for evolutionary tree reconstruction. Although neighbor joining is regarded as the most popular and fastest evolutionary tree reconstruction method [its time complexity is O(n(3)), where n is the number of sequences], it is not sufficiently fast to infer evolutionary trees containing more than a few hundred sequences. To increase the speed of neighbor joining, we herein propose FastNJ, a fast implementation of neighbor joining, which was motivated by RNJ and FastJoin, two improved versions of conventional neighbor joining. The main difference between FastNJ and conventional neighbor joining is that, in the former, many pairs of nodes selected by the rule used in RNJ are joined in each iteration. In theory, the time complexity of FastNJ can reach O(n(2)) in the best cases. Experimental results show that FastNJ yields a significant increase in speed compared to RNJ and conventional neighbor joining with a minimal loss of accuracy.

Citations

Sep 13, 2019·Transboundary and Emerging Diseases·Muddassar HameedZhiyong Ma
May 18, 2018·BMC Bioinformatics·Guilherme P TellesNalvo F Almeida
Oct 21, 2017·Evolutionary Bioinformatics Online·Guan-Jie HuaChuan Yi Tang
Jan 12, 2021·Molecular Therapy. Nucleic Acids·Yan HongJuan Wang

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