Phydms

---------
* Handle stop codons in preferences

* Change default color scheme for logoplots

* Some minor tweaks to reduce underflow

* Some minor doc updates

-------------
* Compatible with either Python 2.7 or Python 3.4 or greater.

* Completely re-write of the implementation the likelihood calculations. We eliminate the dependence on ``Bio++`` and instead use custom coded calculations without derivatives.

* All tree topology inference is eliminated, some options are removed, numerical values are expected to be slightly different, and speed should be greatly enhanced.

-----------
* Added ``--divpressure`` option for analyzing diversifying pressure at sites.

* Added ``--fixationmodel`` option to allow different ways to relate preferences to fixation probabilities.

* In ``phydms_prepalignment``: bug fixes, have ``mafft`` use all available threads, and keep seqs in ``--keepseqs`` regardless of identity to refseq.

* Added ``phydms_testdivpressure``

----------
* Bug fix in ``phydms_prepalignment``

* Added more recent version of ``Bio++`` code

-------
* Added ``phydms_prepalignment`` program.

----------
* Updated docs

* Handle negative MRCAs for ``--dateseqs`` without error

* Added option ``--colormap`` to ``phydms_plotselection``.

* Removed requirements that input sequences be unique in ``alignment``.