CHANGELOG v1.6.6 (9th Nov 2016) Changed citation. Scoary is now available through Zenodo. v1.6.5 (25th Oct 2016) Added the README_pypi.md file so that setup.py can be used to build/install locally if pip not installed. v1.6.4 (18th Oct 2016) Made the permutations algorithm faster by implementing a dynamic cutoff v1.6.3 (14th Oct 2016) Removed OR calculation from PhyloTree class Now prints collapse option to stdout Cleaned up threading method v1.6.2 (13th Oct 2016) 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 v1.6.1 (7th Oct 2016) 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 v1.5.1 (22nd Sep 2016) 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.