Staphylococcus aureus:

PrepareAllPathsInputs.pl DATA_DIR=$PWD PLOIDY=1
RunAllPaths3G PRE=. REFERENCE_NAME=. DATA_SUBDIR=. RUN=allpaths SUBDIR=run

Rhodobacter sphaeroides:

PrepareAllPathsInputs.pl DATA_DIR=$PWD PLOIDY=1
RunAllPaths3G PRE=. REFERENCE_NAME=. DATA_SUBDIR=. RUN=allpaths SUBDIR=run

Human Chromosome 14:

PrepareAllPathsInputs.pl DATA_DIR=$PWD PLOIDY=2
RunAllPaths3G PRE=. REFERENCE_NAME=. DATA_SUBDIR=. RUN=allpaths SUBDIR=run