On Monday, February 4, 2013, Luobin Yang wrote:

Hi, Peter,

Thanks for pointing them out!

The phi-blast and psi-blast actually share the same binary, both use the psiblast program in the NCBI BLAST+ tools. When the option -phi_pattern is used, then it does phi-blast searching.

Best,
Luobin

Could you give a few command line examples of how you typically use psiblast, focussing in the main options only?

I would find that helpful when putting together a new wrapper - since including all the options right away is overwhelming.

Thanks,

Peter