Dynamic Partial Reconfiguration & Direct Bitstream File Manipulation

Altera's tool chain will allow you to perform different parts of the compilation separately. You can ask it to perform the 'assembly' step, the step that creates the .sof file, independently. However, this will be of limited use on its own, assuming you're looking to change source code between iteration cycles.

Quartus II supports incremental compilation, allowing you to 'lock' portions of your design and only re-analyse, fit and assemble the bits that have changed. You don't mention what it is you're intending to change between iterations, but assuming it's source code then this will be the way to go.

Have a look at Altera's documentation on incremental compilation.

http://www.altera.com/support/software/incremental/sof-qts-increment-comp.html (http://www.altera.com/support/software/incremental/sof-qts-increment-comp.html)

Regards,

Alex