NUMBER OF THREADS

ccl
----

Drastic improvement up to 8 CPUs, and minor improvement up to 64.

brassica
---------
slignt decrease in performance as threads increase from 1 to 8.

wotan
-----
substantial improvement in performance up to 4 CPUs


triticum
__________

negligible decrease in performance as threads increase from 1 to 4 CPUs

flamingo
--------
Major improvement in performance as threads increase from 1 to 24


albacore
--------
some improvement in performance as threads increase from 1 to 8


orpheus
--------
small improvement as threads increase from 1 to 4


Conclusion:

The best default is to use the maximum number of CPUs. On many systems there 
significant improvements with number of CPUs, and even on systems with minimal
memory, the hit from overhead with large number of CPUs is not significant.

EVALUE

No significant effect of E-value between 1e-1 and 1e-10 on brassica and ccl

MAX_TARGET_SEQS

No siginficant effect of -max_target_seqs between 500 and 25 on brassica and ccl.