; Sample Phylotyper config file
;

# External programs
[external]
fasttree=/path/to/FastTree
mafft=/path/to/mafft
trimal=/path/to/trimal
makeblastdb=/path/to/makeblastdb ; part of the BLAST+ suite
blastn=/path/to/blastn ; part of the BLAST+ suite
blastx=/path/to/blastx ; part of the BLAST+ suite
blastdbcmd=/path/to/blastdbcmd ; part of the BLAST+ suite

# R settings
[R]
lib=/path/to/local/R/libs/ ; Location where downloaed R packages can be saved
repo=http://cran.stat.sfu.ca/ ; HTTP address of R repository to use for downloading R packages
rscript=/usr/bin/Rscript ; Part of the R suite

# Phylotyper settings
[phylotyper]
prediction_threshold=0.9 ; Cutoff for calling subtype assignments