Efficiently create PSI-BLAST-like PSSMs from very large MSAs

Question

[alquraishi]

I have a multiple sequence alignment that I'd like to turn into a PSI-BLAST-like PSSM. I'm aware of this solution, but unfortunately PSI-BLAST appears to croak on very large alignments (hundreds of thousands of sequences). Are there other tools out there that generate the same PSI-BLAST style PSSM files that can handle very large MSAs?

[Khader Shameer]

We had success in leveraging PSI-BLAST for generating PSSMs for a large number of sequences (See database of PSSM profiles here; publication here). Can you give the specifics of the issues?

[alquraishi]

I have an MSA that has about 200,000 sequences. I ran PSI-BLAST for over 12 hours and it did not finish (on this single MSA). Has your experience been different?