.gitignore
LICENSE
MANIFEST.in
Makefile
README.md
README.rst
logo_300px.png
requirements_dev.txt
setup.cfg
setup.py
carveme/__init__.py
carveme/config.cfg
carveme.egg-info/PKG-INFO
carveme.egg-info/SOURCES.txt
carveme.egg-info/dependency_links.txt
carveme.egg-info/entry_points.txt
carveme.egg-info/not-zip-safe
carveme.egg-info/requires.txt
carveme.egg-info/top_level.txt
carveme/cli/__init__.py
carveme/cli/benchmark.py
carveme/cli/build_universe.py
carveme/cli/carve.py
carveme/cli/gapfill.py
carveme/cli/merge_community.py
carveme/data/benchmark/media_db.tsv
carveme/data/benchmark/biolog/bsub/biolog_carbon.tsv
carveme/data/benchmark/biolog/bsub/biolog_nitrogen.tsv
carveme/data/benchmark/biolog/bsub/biolog_phosphorus.tsv
carveme/data/benchmark/biolog/bsub/biolog_sulfur.tsv
carveme/data/benchmark/biolog/ecol/biolog_carbon.tsv
carveme/data/benchmark/biolog/ecol/biolog_nitrogen.tsv
carveme/data/benchmark/biolog/ecol/biolog_phosphorus.tsv
carveme/data/benchmark/biolog/ecol/biolog_sulfur.tsv
carveme/data/benchmark/biolog/paer/biolog_carbon.tsv
carveme/data/benchmark/biolog/rsol/biolog_carbon.tsv
carveme/data/benchmark/biolog/rsol/biolog_nitrogen.tsv
carveme/data/benchmark/biolog/rsol/biolog_phosphorus.tsv
carveme/data/benchmark/biolog/rsol/biolog_sulfur.tsv
carveme/data/benchmark/biolog/sone/biolog_carbon.tsv
carveme/data/benchmark/biolog/sone/biolog_nitrogen.tsv
carveme/data/benchmark/essentiality/bsub.tsv
carveme/data/benchmark/essentiality/ecol.tsv
carveme/data/benchmark/essentiality/mgen.tsv
carveme/data/benchmark/essentiality/paer.tsv
carveme/data/benchmark/essentiality/sone.tsv
carveme/data/benchmark/fasta/Bsubtilis_168.faa
carveme/data/benchmark/fasta/Bsubtilis_168.tsv
carveme/data/benchmark/fasta/Ecoli_K12_MG1655.faa
carveme/data/benchmark/fasta/Ecoli_K12_MG1655.tsv
carveme/data/benchmark/fasta/M_genitalium_G37.faa
carveme/data/benchmark/fasta/M_genitalium_G37.tsv
carveme/data/benchmark/fasta/Paeruginosa_PAO1.faa
carveme/data/benchmark/fasta/Paeruginosa_PAO1.tsv
carveme/data/benchmark/fasta/Rsolanacearum_GMI1000.faa
carveme/data/benchmark/fasta/Rsolanacearum_GMI1000.tsv
carveme/data/benchmark/fasta/Soneidensis_MR1.faa
carveme/data/benchmark/fasta/Soneidensis_MR1.tsv
carveme/data/benchmark/models/bsub.xml
carveme/data/benchmark/models/ecol.xml
carveme/data/benchmark/models/mgen.xml
carveme/data/benchmark/models/paer.xml
carveme/data/benchmark/models/rsol.xml
carveme/data/benchmark/models/sone.xml
carveme/data/benchmark/results/biolog.tsv
carveme/data/benchmark/results/essentiality.tsv
carveme/data/generated/bigg_gibbs.csv
carveme/data/generated/bigg_gprs.csv.gz
carveme/data/generated/model_specific_data.csv.gz
carveme/data/generated/universe_archaea.xml.gz
carveme/data/generated/universe_bacteria.xml.gz
carveme/data/generated/universe_cyanobacteria.xml.gz
carveme/data/generated/universe_draft.xml.gz
carveme/data/generated/universe_gramneg.xml.gz
carveme/data/generated/universe_grampos.xml.gz
carveme/data/input/bigg_models.csv
carveme/data/input/bigg_proteins.faa
carveme/data/input/biomass_db.tsv
carveme/data/input/equilibrator_compounds.tsv.gz
carveme/data/input/manually_curated.csv
carveme/data/input/media_db.tsv
carveme/data/input/metabolomics_park2016.csv
carveme/data/input/refseq_release_201.tsv.gz
carveme/data/input/unbalanced_metabolites.csv
carveme/reconstruction/__init__.py
carveme/reconstruction/benchmark.py
carveme/reconstruction/carving.py
carveme/reconstruction/diamond.py
carveme/reconstruction/eggnog.py
carveme/reconstruction/gapfilling.py
carveme/reconstruction/ncbi_download.py
carveme/reconstruction/scoring.py
carveme/reconstruction/utils.py
carveme/universe/__init__.py
carveme/universe/bigg_download.py
carveme/universe/curation.py
carveme/universe/thermodynamics.py
docs/.gitignore
docs/Makefile
docs/advanced.rst
docs/conf.py
docs/index.rst
docs/installation.rst
docs/make.bat
docs/requirements.txt
docs/usage.rst
tests/__init__.py
tests/test_carveme.py