[BiO BB] SNP analysis program

[Hongyu Zhang]

Dear all,

I am looking for a SNP analysis program, which is good at

Assemble 
chromats
Allow me to edit 
chromats

Displays mixed 
bases

Displays polymorphisms 
calls



We have looked at Polyphred and Sequencher. Polyphred works well in
Linux/Unix, so it can be wrapped in a shell script to run in batch mode
processing bulk data. It is also in good compatibility with Phred/Phrap
and consed. Sequencher has nice GUI and runs on Windows, which is good
for scientist to do annotation interactively, but I am not sure whether
it can be run in batch mode.

If you have any good suggestions, please let me know. Thanks!


 
Hongyu Zhang, Ph.D.
Computational biologist 
 Ceres Inc., Thousand Oaks, CA
Cell: 805-405-5394
Fax: 866-447-8750