Phykit

- The partition file outputted from the create_concat function has been updated
- Column information in the partition file is as follows:
- column 1: alignment name
- column 2: of taxa present
- column 3: of taxa missing
- column 4: fraction of occupancy
- column 5: names of missing taxa (; separated)

- Fixed bug for thread_dna function when using a ClipKIT log file. Input protein alignment must be the untrimmed alignment.

- Saturation function forces y-intercept to be zero when calculating slope

- Saturation function now uses uncorrected distances instead of pairwise identities

- Verbose pairwise identity reporting separates pairwise identities by tabs and not a dash

- Added function to test for site-wise compositional biases in an alignment. See function compositional_bias_per_site.