Refactor command file writing for code reuse
Refactor phylogeny runner options

Now the phylogeny runner options are set by a flexible function that is
much more readable than the ad hoc way it had been done.
This also makes it easier to incorporate bootstrapping ultimately.
Finish integrating seqboot run into phylogeny run

This consisted of cleaning up the options generation function used in
the case of bootstrapping.
It still does not generate a consensus tree, just a list of generated
trees.
Implement running of consense

There is still no integration with run_phylip
Integrate run_consense into run_phylip
Integrate clean-up of consense output

There are still a few bugs, and hackish things.
When I convert the branch support to branch lengths, I have to add weird
options.
Improve PEP8 compliance

Add docstrings where necessary, among other changes to get pylint to
stop yelling at me so much.
Clean up comments fo easy folding