v1.0.1

• fixed bug in e.coli test (checkm test)
• fixed bug in installation of CheckM from pypi

v1.0.0

• added output format to qa command that writes all marker genes to a fasta file (courtesy of Hunter Cameron)
• added unique node ids to qa output tables
• added --exclude_markers flag to qa command
• fix to remove temporary *.ssi files

v0.9.7

• added unique ids of selected marker sets to CheckM output tables
• improved quality of internal taxonomic labels in reference genome tree

v0.9.6

• fixed bug preventing checkm test from running
• moving towards PEP8 compliance

v0.9.5

• added support for a reduced reference tree through the --reduced-tree argument
• added support to use previously called genes instead of identifying these de novo
• improve handling of data dependencies and server connection through ScreamingBackpack
• improved plots for compatibility with matplotlib v1.4.0
• improved command-line help

v0.9.4

• updated plots
• made marker set refinement on by default
• removed all references to local directories
• updated E.coli test

v0.9.0

Changed pip name to checkm-genome