[Biojava-l] question regarding MSA

[Bo Li]

Hi,

Sorry for the bothering.  I tried the MSA feature by following the link:

http://www.biojava.org/wiki/BioJava:CookBook3:MSA

However, I can't see the symbols like ".", ":", and "*" like I can see  
from the output ClustalW.

So is there a way for users to obtain such information in the output  
from MSA?

Thanks,
Bo Li