This is a program for multiple sequence alignment. It runs faster than any other software if the sequences are similar.

It is developed with JAVA. So make sure JDK 1.6 or higher in your OS, please.



For windows user, improvedcenterstar.exe (166k)

For other user, improvedcenterstar.jar (17.3k)

Source code (82.8k)

Test data (24.7k)



Write the sequences you want to align to a FASTA file, and put it in the same folder with the program.

If you are in windows, go to dos in this folder and run

improvedcenterstar test.txt 1

If you are in other OS, please run

java -jar improvedcenterstar.jar test.txt 1


Here 1 can be omitted or replaced by 0. If you want to align the sequences with high similarity, please use 1(recommended); if the sequences are low similar, you can choose 0 to use common center star method for multiple sequence alignment.


After that, the aligned sequences will be saved in a new created file ‘output.txt’.



Quan Zou, Maozu Guo, Xiaokai Wang, Taotao Zhang. An Algorithm for DNA Multiple Sequence Alignment Based on Center Star Method and Keyword Tree. Acta Electronica Sinica. 2009,37(8):1746-1750

(邹权, 郭茂祖, 王晓凯, 张涛涛. 基于关键字树的DNA多序列星比对算法. 电子学报. 2009,37(8):1746-1750)


If you have any problem or any suggestion, please feel free to contact me.


Quan Zou


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