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HAlign-II is a tool for multiple sequence alignment of amino acid and nucleotide sequences and phylogenetic tree construction aimed for sequence files bigger than one Gb. The software can be used in standalone or in Hadoop cluster mode. HAlign-II contains three types of sequence alignment methods and a large-scale phylogenetic tree construction method based on Apache Spark platform. You can also run HAlign-II on the web server on the clusters in Tianjin University (Spark & Hadoop cluster and NVIDIA K80 GPU cluster). The webserver is accessible from the HAlign-II web pagepage.


Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs


  • Operation: Phylogenetic tree generation; multiple sequence alignment
  • Input: FASTA
  • Output: FASTA
  • Software interface: Command-line user interface; web user interface
  • Language: Java
  • Operating system: Linux, Mac OS X, Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: 2
  • Maturity: Stable
  • Credit: Yaozong Mao, Shixiang Wan, Natural Science Foundation of China (No.61370010)
  • Contact: zouquan _at_
  • Collection: -


Wan S, Zou Q "HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing." Algorithms Mol Biol. 2017 Sep 29;12:25.
PMID: 29026435

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