Multiple Sequence Alignment with Suffix Tree

This project is aimed at improving a part of HAlign2.0, which could align multiple nucleotide sequences fast and accurately.


java -jar halign-stmsa.jar infile

Detailed usage could be found at Github or run the software with optional argument -h.

please note that this software is dependent on java 11 or higher version


Software documentation could be found at Github Wiki.


Source code could be found at Github.

Compiled jar file could be downloaded at Github release page.

Related Tool

We have developed a webpage with a few effects to help do pairwise alignment online with Needleman-Wunsch algorithm.


The software is currently maintained by Chao Jiannan with the help of Prof. Zou.

If you hava any problems, feel free to contact us or submit an issue via Github.