Scoary

- Made the permutations algorithm faster by implementing a dynamic cutoff

- Removed OR calculation from PhyloTree class
- Now prints collapse option to stdout
- Cleaned up threading method

- Collapsing correlated genes is now optional, controlled with the --collapse flag
- Fixed a bug where the collapsing duplicated some genes
- Collapsing is default to False in GUI mode

- Added a GUI, callable as scoary_GUI
- Added post-analysis label-switching permutations, and the option to filter on empirical p-values
- Added multiprocessing to speed up permutations
- Added a second column in the phenotype exampledata
- Adds an outdir option
- Now available through PyPi

- Users can now provide a custom tree that will be used for analysis instead of the internally calculated one.
- Changed the way trees are written to file. Leaf nodes will no longer have "double" distance. The tree files are now also rooted, which allows them to be read by other software
- Fixed some typos and added a lot of exception throwing for when the user is trying strange things, such as pointing to files that don't exist.

- Scoary is now installable via pip! (Thanks go to Anders Goncalves da Silva). The scoary.py script will now be deprecated, but is still available for legacy use. See [Installation] (installation)
- The program now also prints out the filtration options being used for the current analysis.