HAlign-II is a Java based software, which can align multiple nuleotide/protein sequences stand-alone on Hadoop cluster. Hadoop parallel computing environment has a faster alignment speed. Additionally, if a Hadoop cluster environment is not ready, you can use its stand-alone mode to start your work. But when your sequence files are large (more than 1GB), we recommend that you'd better to run on the Hadoop cluster to save valuable time.

Home page: http://lab.malab.cn/soft/halign
Reference: Shixiang Wan and Quan Zou, HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing, Algorithms for Molecular Biology, 2017, 12:25. view

Other implementations:

• MPI: https://github.com/ShixiangWan/MPI-MSA
• CUDA: https://github.com/ShixiangWan/CMSA2

• JDK 1.8
• Hadoop 2.7.2
• Spark 2.0.2
• Intellij IDEA (Maven)

# java -jar HAlign2.1.jar <mode> <input-file> <output-file> <algorithm>

• mode: -localMSA, -localTree.
• input-file: local fasta format file, required.
• output-file: local fasta format file, just a file name, required.
• algorithm: sequence alignment algorithms, required for -localMSA mode, but none for -localTree mode. 0 represents the suffix tree algorithm, the fastest, but only for DNA/RNA; 1 represents the KBand algorithm based BLOSUM62 scoring matrix, only for Protein; 2 represents the KBand algorithm based on affine gap penalty, only for DNA/RNA; 3 represents the trie tree alignment algorithm, but slower and only for DNA/RNA; 4 represents the basic algorithm based the similarity matrix, the slowest and only for DNA/RNA. But it is the most accurate in the case of lower sequences similarity.

# hadoop jar HAlign2.1.jar <mode> <input-file> <output-file> <algorithm>

• mode: -hadoopMSA.
• input_file/output_file/algorithm type: same as stand-alone mode.

# spark-submit --class main HAlign2.1.jar <mode> <input-file> <output-file> <algorithm>

• mode: -sparkMSA, -sparkTree.
• input-file: local fasta format file, required.
• output-file: local fasta format file, just a file name, required.
• algorithm: sequence alignment algorithms, required for -sparkMSA mode, but none for -sparkTree mode. 0 represents the suffix tree algorithm, the fastest, but only for DNA/RNA; 1 represents the KBand algorithm based BLOSUM62 scoring matrix, only for Protein.

• 2020-07-16, version 2.1.2:
  • bug fix
• 2016-11-25, version 2.1.1:
  • Fix some bugs about protein sequences alignment on multi-thread technique.
  • Fix some bugs about file I/O.
• 2016-11-14, version 2.1.0:
  • Add version: comment for english.
• 2016-09-07, version 2.0.0:
  • Basic functions.