aggregate nucleotide substutition model fits into one csv
Split up fasttree and hyphy functionality into separate python files.  Add ability to compare GTR nucleotide substution models using HyPhy.  Add ability to extract GTR rates directly from fasttree logfiles.
Fixed bug where sample name was cutoff in gtr rates  csv file contents
Avoid pickling to debug mpi node-node communication errors that result in corruption of message sent to slave
Fixed mpi node-node communication bug - master needs to keep track of both send MPI.Request and receive MPI.Request objects since they have separate buffers with different info.  send MPI.Request contains buffer with work args for the slave.  receive MPI.request contains buffer with slave's response.
Removed copy of code that uses array.array instead of python pickling for mpi communication
add a smoothing distance for dn/ds with default 0 codon positions.
Fixed bug where weighted average dn/ds was not ignoring window-sites where dn/ds is None because there are zero observed synonymous substitutions.
Fixed divide by zero error
Fixed another divide by zero error.  readded smoothing distance hack.  Hardcoded smoothing distance to 15
Remove simulation data files from git
Remove simulation test html figures
Fixed bug where nan returns from multisite dnds.  Added smoothing distance as parameter in sliding window
Remove redundant line in slice_miseq.  Add new function to calculate non-gapped coverage in each position in multiple sequence aligned fasta file
Find concordance correlation coefficient
Remove png files
Fixed labels for concordance coefficient stats.  Added graphs for simple dn/ds.
Add calculations for simple dn/ds  (total nonsynonymous substitutions / total synonymous substitutions), where values are not normalized by expected values.

Add smoothing distance parameter to unit tests.
Minor change to take in scaling factors via commandline
Merge branch 'mutation_rates'

Conflicts:
	sliding_window_tree.py
- Add ability to tabulate GTR rates from fasttree logs
- Add ability to tabulate nucleotide substitution rates from various nucleotide substitution models
- Cache both send & receive requests in the primary process until the replica is done.
- Fixed bugs where site dn/ds were not weighted by reads, substitutions, etc.
- Moved all hyphy work to hyphy_handler.py
- Moved all fasttree work to fasttree_handler.py
- Removed the knitr generated png files from the R unit test graphing