I would like to simulate sequences for a population undergoing mutation and recombination in the presence of strong selection. I would like to be able to specify an arbitrary fitness landscape, hopefully with some nice parameterization. I don’t want to start from scratch and write a forward time simulator. I’m hoping to get some feedback from you all about how to do this.
Here is what I have seen so far:
@tgvaughan has written the very nice looking MASTER. However, my impression is that this involves a fixed number of types, and relative fitness is implicitly defined by the master equations determining how those types leave progeny. I would like a mutant to have a different fitness than its predecessor.
I found a software package called VIRAPOPS which is distributed as binaries. I contacted the author and the f77 code is not open-source. Not going to use a simulator that I can’t look at under the hood of, thankyouverymuch.
There is a cool looking package called forqs that is open source C++, but which is really designed with diploid populations that recombine via crossing-over in mind. I’ve been in touch with that author, who was very friendly and helpful, but it would require some deep recoding, or some abuse.
Am I forgetting something obvious?