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

被引：16
|
作者：
Tang, Furong [1 ,2 ]
Chao, Jiannan [1 ,3 ]
Wei, Yanming [4 ]
Yang, Fenglong [5 ]
Zhai, Yixiao [3 ]
Xu, Lei [2 ]
Zou, Quan [1 ,3 ]
机构：
[1] Univ Elect Sci & Technol China, Yangtze Delta Reg Inst Quzhou, Quzhou, Peoples R China
[2] Shenzhen Polytech, Sch Elect & Commun Engn, Shenzhen, Peoples R China
[3] Univ Elect Sci & Technol China, Inst Fundamental & Frontier Sci, Chengdu, Peoples R China
[4] Xidian Univ, Sch Comp Sci & Technol, Xian, Peoples R China
[5] Fujian Med Univ, Sch Med Technol & Engn, Fuzhou, Peoples R China
来源：
MOLECULAR BIOLOGY AND EVOLUTION | 2022年 / 39卷 / 08期
基金：
中国博士后科学基金; 中国国家自然科学基金;
关键词：
multiple sequence alignment; suffix tree; center star strategy; common substring; substring selection; ALGORITHM;
D O I：
10.1093/molbev/msac166
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
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).
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页数：5
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