HAlign 3: Fast Multiple Alignment of Ultra-Large Numbers of Similar DNA/RNA Sequences

Furong Tang; Jiannan Chao; Yanming Wei; Fenglong Yang; Yixiao Zhai; Lei Xu; Quan Zou

doi:10.1093/molbev/msac166

HAlign 3: Fast Multiple Alignment of Ultra-Large Numbers of Similar DNA/RNA Sequences

Mol Biol Evol. 2022 Aug 3;39(8):msac166. doi: 10.1093/molbev/msac166.

Authors

Furong Tang^{1

2}, Jiannan Chao^{1

3}, Yanming Wei⁴, Fenglong Yang⁵, Yixiao Zhai³, Lei Xu², Quan Zou^{1

3}

Affiliations

¹ Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China.
² School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China.
³ Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
⁴ School of Computer Science and Technology, Xidian University, Xi'an, China.
⁵ School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China.

Abstract

HAlign is a cross-platform program that performs multiple sequence alignments based on the center star strategy. Here we present two major updates of HAlign 3, which helped improve the time efficiency and the alignment quality, and made HAlign 3 a specialized program to process ultra-large numbers of similar DNA/RNA sequences, such as closely related viral or prokaryotic genomes. HAlign 3 can be easily installed via the Anaconda and Java release package on macOS, Linux, Windows subsystem for Linux, and Windows systems, and the source code is available on GitHub (https://github.com/malabz/HAlign-3).

Keywords: center star strategy; common substring; multiple sequence alignment; substring selection; suffix tree.

Publication types

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

MeSH terms

Algorithms*
Base Sequence
DNA / genetics
Sequence Alignment
Software*

Substances

DNA