#This file is meant to be edited in your own distribution of MANTIS

#######DEFAULT PATHS#######
#You can add custom paths here, otherwise they will be set to default values
#default_ref_folder=
#####<custom_ref_folder> defines the folder where Mantis will look for MULTIPLE custom HMMs or DMND. Each HMM should be contained within a folder, such that the path will look something like this: /path/to/custom_ref_folder/custom1/custom1.hmm
#custom_ref_folder=
# dmnd or hmm
nog_ref=dmnd
#nog_ref_folder=
#pfam_ref_folder=
#kofam_ref_folder=
#ncbi_ref_folder=
#tcdb_ref_folder=
#nog_tax=NCBI_ID

#####Make sure the  names of the weights correspond to the path of the hmms
#####example: <NOGT>_ref_folder should be <NOGT>_weight
#####example: custom_ref=path/to/customHMM.hmm should be customHMM_weight
nog_weight=0.8
pfam_weight=0.9


#######CUSTOM REFERENCES#######
#####<custom_ref> defines the folder or file where Mantis will look for a SINGLE custom reference (HMM or DMND). The path will look something like this: /path/to/custom1/custom1.hmm or /path/to/custom1/
#custom_ref=path/to/hmm/custom1.hmm
#custom_ref=path/to/hmm/custom2.dmnd
#to set the weight, simply add a line with the hmm file name followed by _weight , for example, if the file path is path/to/hmm/custom1.hmm, then you take the name of the file <custom1> without the extension and set the weight like so:
#custom1_weight=0.5

