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.

Luobin

On Mon, Feb 4, 2013 at 11:14 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang <yangluob@isu.edu> wrote:
> Hi, Peter,
>
> What difficulties did you see to include psi-blast and phi-blast when you
> were working on the other programs in the NCBI+ suite? I would be interested
> in creating a tool configuration file for each of these two.
>
> Thanks,
> Luobin

Hi Luobin,

At first glance, the binaries for psiblast, rpsblast, and rpstblastn don't
look too different for wrapping. We would need to define a third loc
file for the RPS BLAST domain databases (like the existing loc files
for nucleotide and protein databases).

However, I'm not immediately sure where phi-blast existing with the
standalone NCBI BLAST+ tools. Do you know?

Peter