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Multiple sequence alignment (MSA) plays a key role in biological sequenceanalyses, especially in phylogenetic tree construction. Extreme increase innext-generation sequencing results in shortage of efficient ultra-largebiological sequence alignment approaches for coping with different sequencetypes. Distributed and parallel computing represents a crucial technique foraccelerating ultra-large sequence analyses. Based on HAlign and Sparkdistributed computing system, we implement a highly cost-efficient andtime-efficient HAlign-II tool to address ultra-large multiple biologicalsequence alignment and phylogenetic tree construction. After comparing withmost available state-of-the-art methods, our experimental results indicate thefollowing: 1) HAlign-II can efficiently carry out MSA and constructphylogenetic trees with ultra-large biological sequences; 2) HAlign-II showsextremely high memory efficiency and scales well with increases in computingresource; 3) HAlign-II provides a user-friendly web server based on ourdistributed computing infrastructure. HAlign-II with open-source codes anddatasets was established at http://lab.malab.cn/soft/halign.

HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing