6008 / SMCJava

SMCJava

Usage:

java -jar SMCalpha.jar abundance_species_equal.txt

The file contains pair-end sequence

More Usage:

java -jar SMCalpha.jar [OPTION] abundance_species_equal.txt

Options:

-a:	The value followed will be the alpha parameter

   	Default value 0.0000001
   	
-n:	The value followed will be the sample number parameter

   	Default value 100
   	
-m:	The value followed will be the alpha parameter

   	Default value 1
   	
-t:	The value followed will be the threshold parameter

   	Default value 0.9
   	
-g:	Choose to use GC order the origin datas first

More and more Usage:

1. default java -jar SMCalpha.jar abundance_species_equal.txt

2. with parameters java -jar SMCalpha.jar -n 100 -a 0.001 abundance_species_equal.txt

3. with Java parameters (When out of memory) java -Xms1024m -jar SMCalpha.jar -n 100 -a 0.001 abundance_species_equal.txt