0.1.5
- fixed mering issue

0.1.4
- added prune method

0.1.3
- modified main.py to have Python 3 print statements

0.1.2
- updated shebang to Python 3

0.1.1
- added CM data files to repository

0.1.0
- initial migration to Python 3

0.0.55
- added rm_support
- bootstrap command will not look for files with the extension '.treefile'

0.0.54
- modified PD calculations when ingroup does not encompass root node; this
  makes PD a rooted tree calculation, but this is probably best for most
  situations
- simplified interface to PD calculations to remove notion of representative genomes

0.0.53
- better handling of support values when 'stripping' a tree

0.0.52
- modified cluster_de_novo to ensure all genomes as assigned to the closest type genome
- fixed synonym table: species were being indicated as synonyms of multiple species (e.g. Shigella boydii)

0.0.51
- added --rnd_type_genome option for evaluating impact of type genome selection on de novo clusters

0.0.50
- added --gamma option to bootstrap command so it isn't automatically used

0.0.49
- used for GTDB r89
- added QC exception list to qc_genomes command
- added species classification exception list to qc_genomes command
- added species classification exception list to select_type_genomes command
- added species classification exception list to cluster_named_types command
- added GTDB type genomes exception list to select_type_genomes command
- added species type genome radius information to file indicating species clusters
- simplified interface to cluster_user as species ANI radius information is now in cluster file
- stripped 'Candidatus' from all species names

0.0.48
- added type species of genus information for resolving priority of species with same publication date
- changed {manual_curation} to {unresolved}
- changed determination of genus name for de novo species clusters to consider most common genus name in cluster
- added checks to ensure genomes marked as assembled from type material or NCBI representative genomes as not actually a subspecies

0.0.47
- initial implementation of filtering of percentage of bac120 or ar122 marker genes

0.0.46
- initial type genome workflow for GTDB r89

0.0.45
- improved dereplication workflow for GTDB r89

0.0.44
- add method to dump 5S, 16S, and 23S sequences to file

0.0.43
- improvements to code for assigning genomes to canonical genome set 

0.0.42
- initial implementation of code to assign genomes to canonical genome set 

0.0.41
- fixed bug with parsing contig length from SSU file

0.0.40
- fixed issue with rerooting trees with bootstraps between [0, 1]

0.0.39
- added GTR model when inferring SSU or LSU trees

0.0.38
- new method for selecting GTDB representatives

0.0.37
