Upon request, any HMM profiles database (for instance pVOGs used for training reference datasets) can be used to provide additional signal while running PhiSpy.
Also:
updated README files with instructions of phmms search and making training sets
fixed extra headers in generated training sets with make_training_sets.py
updated one reference genome with indicated prophage remnants
retrained reference datasets to include signal from pVOGs search
added a simple script to plot PNG files from test or training sets
phmms search updates input GenBank file and optionally adds /color qualifier to CDS with phmms hits for more convenient manual genome inspection with Artemis
Upon request, any HMM profiles database (for instance pVOGs used for training reference datasets) can be used to provide additional signal while running PhiSpy.
Also: