This is a program for aligning multiple homologous sequences. The performance of the program is great. You can use the program in Eclipse IDE with spark environment. Also your can run it in the Linux command line as:
./bin/spark-submit --class main --master msa.jar <input_file> The spark-submit is the tool to run spark program with submitting a jar file. So you may need to run it in the spark environment. You can find the msa.jar at root of the folder.