Title: HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing,
Abstract: Multiple sequence alignment (MSA) plays a key role in biological sequence
analyses, especially in phylogenetic tree construction. Extreme increase in
next-generation sequencing results in shortage of efficient ultra-large
biological sequence alignment approaches for coping with different sequence
types. Distributed and parallel computing represents a crucial technique for
accelerating ultra-large sequence analyses. Based on HAlign and Spark
distributed computing system, we implement a highly cost-efficient and
time-efficient HAlign-II tool to address ultra-large multiple biological
sequence alignment and phylogenetic tree construction. After comparing with
most available state-of-the-art methods, our experimental results indicate the
following: 1) HAlign-II can efficiently carry out MSA and construct
phylogenetic trees with ultra-large biological sequences; 2) HAlign-II shows
extremely high memory efficiency and scales well with increases in computing
resource; 3) HAlign-II provides a user-friendly web server based on our
distributed computing infrastructure. HAlign-II with open-source codes and
datasets was established at this http URL.