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
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).
Topics & Concepts
BiologyComputational biologyRNAOperating systemSource codeProcess (computing)GenomeCode (set theory)JavaSequence (biology)DNAComputer scienceGeneticsProgramming languageSet (abstract data type)GeneGenomics and Phylogenetic StudiesBacteriophages and microbial interactionsAlgorithms and Data Compression