Update with citation for new model and add -pps flag

[mariodosreis]

@tamuri The new paper in MBE should be cited in the README and in other documentation as appropriate. A -pps flag (for persistent positive selection) should be added in addition to the -fds flag, to activate the new swMutSel-PPS model.

[mariodosreis]

Hi @tamuri , any updates on this issue and associated pull request?

[tamuri]

Sorry, I need to work on merging the source. The PPS work was forked earlier and then work continued on this repo. There are a few conflicts that need to be resolved.

[tamuri]

In the meantime, here's PPS release