LICENSE.txt
MANIFEST.in
README.md
setup.cfg
setup.py
menace/__init__.py
menace/__main__.py
menace.egg-info/PKG-INFO
menace.egg-info/SOURCES.txt
menace.egg-info/dependency_links.txt
menace.egg-info/entry_points.txt
menace.egg-info/requires.txt
menace.egg-info/top_level.txt
menace/bin/PTRMatrix.py
menace/bin/__init__.py
menace/bin/__init__.pyc
menace/bin/addStrainCoverage.py
menace/bin/buildHelper.sh
menace/bin/changeTID.sh
menace/bin/fetchSeq.py
menace/bin/fetchSeq.pyc
menace/bin/gurobi_assign.py
menace/bin/interp.pl
menace/bin/loadmodules.sh
menace/bin/mainBuildBowtie2.sh
menace/bin/mainBuildGem.sh
menace/bin/mainBuildbowtie2.sh
menace/bin/mainBuildgem.sh
menace/bin/piecewiseFit.py
menace/bin/prune_ref.py
menace/bin/refSel.py
menace/extra/.DS_Store
menace/extra/Community Sampling-Copy1.ipynb
menace/extra/Community Sampling.ipynb
menace/extra/Community Sampling.ipynb copy
menace/extra/__init__.py
menace/extra/accLoc.csv
menace/extra/bibPipe.sh
menace/extra/changefn.sh
menace/extra/compareSim.pl
menace/extra/concatenateFasta.sh
menace/extra/generalizeReferences.pl
menace/extra/getSubalignments.pl
menace/extra/menace_run.ipynb
menace/extra/mutate_seq.py
menace/extra/origins.txt
menace/extra/project.conf.example
menace/extra/ptrc_commands.sh
menace/extra/referenceACC.txt
menace/extra/referenceACClong.txt
menace/extra/setup.py
menace/extra/.ipynb_checkpoints/Community Sampling-Copy1-checkpoint.ipynb
menace/extra/.ipynb_checkpoints/Community Sampling-checkpoint.ipynb
menace/extra/.ipynb_checkpoints/menace_run-checkpoint.ipynb
menace/extra/DoriC/bacteria_record.dat
menace/extra/DoriC/bacteria_seq.fas
menace/extra/DoriC/DoriCdb/DoriC.nhr
menace/extra/DoriC/DoriCdb/DoriC.nin
menace/extra/DoriC/DoriCdb/DoriC.nog
menace/extra/DoriC/DoriCdb/DoriC.nsd
menace/extra/DoriC/DoriCdb/DoriC.nsi
menace/extra/DoriC/DoriCdb/DoriC.nsq
menace/lib/Community.py
menace/lib/__init__.py
menace/templates/__init__.py
menace/templates/jobscript
menace/templates/jobscript_local
menace/templates/project.conf
menace/test/__init__.py
menace/test/comm00_1.fastq
menace/test/comm00_2.fastq
menace/test/searchStrings