Optimizing taxon addition order and branch lengths in the construction of phylogenetic trees using maximum likelihood

Yourim Yoon; Yong-Hyuk Kim

doi:10.1142/S0219720020500031

Optimizing taxon addition order and branch lengths in the construction of phylogenetic trees using maximum likelihood

J Bioinform Comput Biol. 2020 Apr;18(2):2050003. doi: 10.1142/S0219720020500031. Epub 2020 May 6.

Authors

Yourim Yoon¹, Yong-Hyuk Kim²

Affiliations

¹ Department of Computer Engineering, College of Information Technology, Gachon University, 1342 Seongnamdaero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Republic of Korea.
² School of Software, Kwangwoon University, 20 Kwangwoon-ro, Nowon-gu, Seoul 01897, Republic of Korea.

PMID: 32372712
DOI: 10.1142/S0219720020500031

Abstract

Taxon addition order and branch lengths are optimized by genetic algorithms (GAS) within the fastDNAml algorithm for constructing phylogenetic trees of high likelihood. Results suggest that optimizing the order in which taxa are added improves the likelihood of the resulting trees.

Keywords: Phylogenetic tree; branch length; genetic algorithm; maximum likelihood; taxon addition order.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Animals
DNA, Mitochondrial
Databases, Genetic
HIV-1 / genetics
Humans
Likelihood Functions*
Mutation Rate
Phylogeny*

Substances

DNA, Mitochondrial