COPYING.txt
MANIFEST.in
README.txt
ez_setup.py
setup.py
bin/petri
bin/pyk-analyze
bin/pyk-compare
bin/pyk-comparison-graph
bin/pyk-mass-run
bin/pyk-profile
bin/pyk-publication-graph
bin/pyk-run
bin/pyk-test
docs/Makefile
docs/index.rst
docs/dev/building.rst
docs/dev/contents.rst
docs/dev/workflow.rst
docs/ref/conf.rst
docs/ref/data-format.rst
docs/ref/genome.rst
docs/ref/modules.rst
docs/ref/other_config_files.rst
docs/ref/petri.rst
docs/ref/sim/comp.rst
docs/ref/sim/env.rst
docs/ref/sim/fam.rst
docs/ref/sim/gen.rst
docs/ref/sim/org.rst
docs/ref/sim/sim.rst
docs/ref/test/test.rst
docs/ref/utils/analysis.rst
docs/ref/utils/comparison.rst
docs/ref/utils/globals.rst
docs/ref/utils/pics/ancestry.png
docs/ref/utils/pics/chemical_complexity.png
docs/ref/utils/pics/chemicals.png
docs/ref/utils/pics/comp_perc_func.png
docs/ref/utils/pics/complex_diversity.png
docs/ref/utils/pics/complexes.png
docs/ref/utils/pics/complexity.png
docs/ref/utils/pics/fam_length.png
docs/ref/utils/pics/fam_size.png
docs/ref/utils/pics/fitness.png
docs/ref/utils/pics/genome.png
docs/ref/utils/pics/invented_complexes.png
docs/ref/utils/pics/percent_functional.png
docs/ref/utils/pics/time_spent.png
docs/tut/deprecated.rst
docs/tut/installing.rst
docs/tut/intro.rst
docs/tut/petri.rst
docs/tut/running.rst
docs/tut/pics/10plot.png
docs/tut/pics/1plot.png
docs/tut/pics/analyze.png
docs/tut/pics/run.png
pykaryote/__init__.py
pykaryote.egg-info/PKG-INFO
pykaryote.egg-info/SOURCES.txt
pykaryote.egg-info/dependency_links.txt
pykaryote.egg-info/requires.txt
pykaryote.egg-info/top_level.txt
pykaryote/configs/cmp.cfg
pykaryote/configs/master.cfg
pykaryote/configs/sim.cfg
pykaryote/petri/__init__.py
pykaryote/petri/master.py
pykaryote/petri/tags.py
pykaryote/petri/worker.py
pykaryote/petri/config/petri_batch.cfg
pykaryote/petri/config/petri_settings.cfg
pykaryote/sim/__init__.py
pykaryote/sim/complexes.c
pykaryote/sim/complexes.pxd
pykaryote/sim/complexes.pyx
pykaryote/sim/environment.c
pykaryote/sim/environment.pyx
pykaryote/sim/families.c
pykaryote/sim/families.pyx
pykaryote/sim/genome.c
pykaryote/sim/genome.pyx
pykaryote/sim/organism.c
pykaryote/sim/organism.pyx
pykaryote/sim/simulation.c
pykaryote/sim/simulation.pyx
pykaryote/test/__init__.py
pykaryote/test/test.py
pykaryote/test/test_data/TestTimeSpentInFlat-sim.cfg
pykaryote/test/test_data/TestTimeSpentInGaussian-sim.cfg
pykaryote/test/test_data/get_config_2_cmp.cfg
pykaryote/test/test_data/get_config_cmp.cfg
pykaryote/test/test_data/make_config.cfg
pykaryote/test/test_data/testEnvironment-sim.cfg
pykaryote/test/test_data/testEnvironmentDraw-sim.cfg
pykaryote/test/test_data/testInitGlobals-sim.cfg
pykaryote/test/test_data/analyzer_quick_read/sim.cfg
pykaryote/test/test_data/analyzer_quick_read/ann0/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann0/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann0/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann1/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann1/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann1/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann10/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann10/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann10/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann11/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann11/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann11/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann2/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann2/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann2/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann3/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann3/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann3/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann4/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann4/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann4/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann5/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann5/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann5/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann6/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann6/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann6/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann7/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann7/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann7/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann8/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann8/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann8/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_quick_read/ann9/complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann9/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_quick_read/ann9/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/10ancestors
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/1ancestors
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/3ancestors
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/chemical_complexity
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/chemicals
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/complex_diversity
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/complexes
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/complexes_invented
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/complexity_avg
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/component_percent_functional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/environment.npy
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/failed_builds
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/family_lengths
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/family_sizes
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/fitness_avg
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/gen_time
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/genome_length_avg
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/irreducible_complexity_avg
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_complexes_current
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_complexes_current_functional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_complexes_current_nonfunctional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_complexes_ever
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_complexes_ever_functional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_complexes_ever_nonfunctional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_families_current
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_families_current_functional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_families_current_nonfunctional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_families_ever
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_families_ever_functional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/num_families_ever_nonfunctional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/percent_functional
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/seed
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/time_spent
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/total_runtime
pykaryote/test/test_data/analyzer_variable_length/run-0/analyzer/used.cfg
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/10ancestors
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/1ancestors
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/3ancestors
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/chemical_complexity
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/chemicals
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/complex_diversity
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/complexes
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/complexes_invented
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/complexity_avg
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/component_percent_functional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/environment.npy
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/failed_builds
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/family_lengths
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/family_sizes
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/fitness_avg
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/gen_time
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/genome_length_avg
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/gens_until_complexity_avg
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/gens_until_genome_length_avg
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/irreducible_complexity_avg
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_complexes_current
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_complexes_current_functional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_complexes_current_nonfunctional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_complexes_ever
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_complexes_ever_functional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_complexes_ever_nonfunctional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_families_current
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_families_current_functional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_families_current_nonfunctional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_families_ever
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_families_ever_functional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/num_families_ever_nonfunctional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/percent_functional
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/seed
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/time_spent
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/total_runtime
pykaryote/test/test_data/analyzer_variable_length/run-1/analyzer/used.cfg
pykaryote/test/test_data/pyk-utils/cmp.cfg
pykaryote/test/test_data/pyk-utils/profile-cmp.cfg
pykaryote/test/test_data/pyk-utils/profile-sim.cfg
pykaryote/test/test_data/pyk-utils/test.cfg
pykaryote/utils/__init__.py
pykaryote/utils/analysis.py
pykaryote/utils/comparison.py
pykaryote/utils/environment_draw.py
pykaryote/utils/globals.py