MANIFEST.in
README.txt
README_SETUP.txt
aksetup_helper.py
configure.py
setup.cfg
setup.py
c++/defs.cpp
c++/steme_defs_pch.h
c++/steme_python_pch.h
c++/FAST/HS-algorithm.h
c++/FAST/HS-list-shift.cpp
c++/FAST/HS-options.h
c++/FAST/HS.cpp
c++/FAST/HS.h
c++/FAST/basic_pruning.cpp
c++/FAST/basic_pruning.h
c++/FAST/brent.h
c++/FAST/complex.h
c++/FAST/convolution.cpp
c++/FAST/convolution.h
c++/FAST/entropy-combined.cpp
c++/FAST/entropy-combined.h
c++/FAST/entropy-test.cpp
c++/FAST/entropy.cpp
c++/FAST/entropy.h
c++/FAST/extended_exponent.h
c++/FAST/fft.cpp
c++/FAST/fft.h
c++/FAST/fftw3.h
c++/FAST/list.h
c++/FAST/llr_score.cpp
c++/FAST/llr_score.h
c++/FAST/me-test.cpp
c++/FAST/minimize.cpp
c++/FAST/minimize.h
c++/FAST/mnbrak.h
c++/FAST/motif_evaluator.cpp
c++/FAST/motif_evaluator.h
c++/FAST/multi_pmf.h
c++/FAST/multinom_prob.cpp
c++/FAST/multinom_prob.h
c++/FAST/naive_enumeration.cpp
c++/FAST/theta_fns.cpp
c++/FAST/theta_fns.h
c++/FAST/utils.cpp
c++/FAST/utils.h
c++/FAST/wisdom
c++/hmm/hmm/baum_welch.h
c++/hmm/hmm/consensus.h
c++/hmm/hmm/count_mers.h
c++/hmm/hmm/defs.h
c++/hmm/hmm/forward_backward.h
c++/hmm/hmm/markov_order.h
c++/hmm/hmm/model.h
c++/hmm/hmm/model_conversion.h
c++/hmm/hmm/model_state.h
c++/hmm/hmm/parameters.h
c++/hmm/hmm/pssm_model.h
c++/hmm/hmm/python.h
c++/hmm/hmm/sample.h
c++/hmm/hmm/simple_pssm.h
c++/hmm/hmm/training.h
c++/hmm/hmm/viterbi.h
c++/hmm/hmm/viterbi_training.h
c++/hmm/multi-array-speed-test/multi-array-speed-test.cpp
c++/hmm/myrrh/myrrh/application.h
c++/hmm/myrrh/myrrh/assert.h
c++/hmm/myrrh/myrrh/bit_set.h
c++/hmm/myrrh/myrrh/chain_iterator.h
c++/hmm/myrrh/myrrh/defs.h
c++/hmm/myrrh/myrrh/fpu.h
c++/hmm/myrrh/myrrh/math.h
c++/hmm/myrrh/myrrh/seqan_boost_range_adaptors.h
c++/hmm/myrrh/myrrh/serialisable.h
c++/hmm/myrrh/myrrh/store_n_best.h
c++/hmm/myrrh/myrrh/suffix_tree.h
c++/hmm/myrrh/myrrh/suffix_tree_graph.h
c++/hmm/myrrh/myrrh/trie.h
c++/hmm/myrrh/myrrh/type_names.h
c++/hmm/myrrh/myrrh/types.h
c++/hmm/myrrh/myrrh/python/boost_function.h
c++/hmm/myrrh/myrrh/python/boost_range.h
c++/hmm/myrrh/myrrh/python/convert.h
c++/hmm/myrrh/myrrh/python/multi_array_to_numpy.h
c++/hmm/myrrh/myrrh/python/numpy.h
c++/hmm/myrrh/myrrh/python/numpy_converter.h
c++/hmm/myrrh/myrrh/python/pyitl.h
c++/hmm/myrrh/myrrh/python/pyitl_impl.h
c++/hmm/myrrh/myrrh/python/registry.h
c++/hmm/myrrh/myrrh/python/tuple.h
c++/hmm/myrrh/myrrh/python/seqan/container.h
c++/hmm/myrrh/myrrh/python/seqan/defs.h
c++/hmm/myrrh/myrrh/python/seqan/index.h
c++/hmm/myrrh/myrrh/python/seqan/iterator.h
c++/hmm/myrrh/myrrh/python/seqan/segment.h
c++/hmm/myrrh/myrrh/python/seqan/string.h
c++/hmm/myrrh/myrrh/serialize/multi_array.h
c++/hmm/myrrh/myrrh/serialize/optional.h
c++/hmm/myrrh/src/application.cpp
c++/hmm/myrrh/src/python/man_module.cpp
c++/hmm/myrrh/src/python/multi_array_to_numpy.cpp
c++/hmm/myrrh/src/python/pyitl_module.cpp
c++/hmm/myrrh/src/python/seqan_module.cpp
c++/hmm/myrrh/src/sandbox/seqan_test.cpp
c++/hmm/myrrh/test/test_bit_set.cpp
c++/hmm/myrrh/test/test_chain_iterator.cpp
c++/hmm/myrrh/test/test_python_boost_range.cpp
c++/hmm/myrrh/test/test_python_numpy_converter.cpp
c++/hmm/myrrh/test/test_seqan_adaptors.cpp
c++/hmm/myrrh/test/test_store_best_n.cpp
c++/hmm/myrrh/test/test_suffix_tree.cpp
c++/hmm/myrrh/test/test_trie.cpp
c++/hmm/myrrh/test/test_type_names.cpp
c++/hmm/src/hmm-pch.h
c++/hmm/src/python_markov_order.cpp
c++/hmm/src/python_model.cpp
c++/hmm/src/python_model_by_states.cpp
c++/hmm/src/python_module_fpu.cpp
c++/hmm/src/python_module_hmm.cpp
c++/hmm/src/python_simple_pssm.cpp
c++/hmm/src/sandbox/multi_array_resize.cpp
c++/hmm/src/test/hmm_test.cpp
c++/hmm/src/test/test.h
c++/hmm/src/test/test_consensus.cpp
c++/hmm/src/test/test_count_mers.cpp
c++/hmm/src/test/test_hmm_ll_increases.cpp
c++/hmm/src/test/test_hmm_model.cpp
c++/hmm/src/test/test_markov_order.cpp
c++/hmm/src/test/test_serialisation.cpp
c++/include/steme.h
c++/include/pvalues/bejerano.h
c++/include/pvalues/calculator.h
c++/include/pvalues/defs.h
c++/include/pvalues/hirji_shifted.h
c++/include/steme/background_model.h
c++/include/steme/background_model_on_the_fly.h
c++/include/steme/binding_model.h
c++/include/steme/data.h
c++/include/steme/defs.h
c++/include/steme/descender.h
c++/include/steme/descender_preferred_order.h
c++/include/steme/em.h
c++/include/steme/find_best_w_mers.h
c++/include/steme/find_instances.h
c++/include/steme/markov.h
c++/include/steme/meme.h
c++/include/steme/model.h
c++/include/steme/seqan_types.h
c++/include/steme/significance.h
c++/include/steme/spec_default.h
c++/include/steme/spec_genome.h
c++/include/steme/start_finder.h
c++/include/steme/todo.h
c++/include/steme/w_mer_evaluation.h
c++/indexing_suite_v2/indexing_suite/algorithms.hpp
c++/indexing_suite_v2/indexing_suite/container_proxy.hpp
c++/indexing_suite_v2/indexing_suite/container_suite.hpp
c++/indexing_suite_v2/indexing_suite/container_traits.hpp
c++/indexing_suite_v2/indexing_suite/deque.hpp
c++/indexing_suite_v2/indexing_suite/element_proxy.hpp
c++/indexing_suite_v2/indexing_suite/element_proxy_traits.hpp
c++/indexing_suite_v2/indexing_suite/int_slice_helper.hpp
c++/indexing_suite_v2/indexing_suite/iterator_range.hpp
c++/indexing_suite_v2/indexing_suite/iterator_traits.hpp
c++/indexing_suite_v2/indexing_suite/list.hpp
c++/indexing_suite_v2/indexing_suite/map.hpp
c++/indexing_suite_v2/indexing_suite/methods.hpp
c++/indexing_suite_v2/indexing_suite/multimap.hpp
c++/indexing_suite_v2/indexing_suite/pair.hpp
c++/indexing_suite_v2/indexing_suite/proxy_iterator.hpp
c++/indexing_suite_v2/indexing_suite/python_iterator.hpp
c++/indexing_suite_v2/indexing_suite/set.hpp
c++/indexing_suite_v2/indexing_suite/shared_proxy_impl.hpp
c++/indexing_suite_v2/indexing_suite/slice.hpp
c++/indexing_suite_v2/indexing_suite/slice_handler.hpp
c++/indexing_suite_v2/indexing_suite/suite_utils.hpp
c++/indexing_suite_v2/indexing_suite/value_traits.hpp
c++/indexing_suite_v2/indexing_suite/vector.hpp
c++/indexing_suite_v2/indexing_suite/visitor.hpp
c++/indexing_suite_v2/indexing_suite/workaround.hpp
c++/meme/lib.c
c++/meme/likelihood.cpp
c++/pvalues/bejerano.cpp
c++/pvalues/fast.cpp
c++/pvalues/hirji_shifted_main.cpp
c++/pvalues/meme.cpp
c++/pvalues/parse.cpp
c++/pvalues/pval.cpp
c++/pvalues/pvalue_test_defs.cpp
c++/pvalues/pvalue_test_defs.h
c++/pvalues/shifted_hirji.cpp
c++/pvalues/test_pval.cpp
c++/pvalues/test_pvalue_speeds.cpp
c++/python/module_index.cpp
c++/python/module_sandbox.cpp
c++/python/module_stempy.cpp
c++/python/python_bg.cpp
c++/python/python_bs.cpp
c++/python/python_data.cpp
c++/python/python_descender.cpp
c++/python/python_em.cpp
c++/python/python_find_best_w_mers.cpp
c++/python/python_find_instances.cpp
c++/python/python_llr_pvalues.cpp
c++/python/python_markov.cpp
c++/python/python_meme.cpp
c++/python/python_model.cpp
c++/python/python_seqan.cpp
c++/python/python_significance.cpp
c++/python/python_start_finder.cpp
c++/python/python_utility.cpp
c++/python/steme.cpp
c++/python/steme_python_defs.h
c++/sandbox/find_best_w_mer_speed.cpp
c++/sandbox/multi_array_sandbox_negative_stride.cpp
c++/sandbox/pthread-static.cpp
c++/sandbox/sandbox_ambiguous_if_else.cpp
c++/sandbox/seqan_read_fasta.cpp
c++/sandbox/seqan_sandbox_abs_freq.cpp
c++/sandbox/seqan_sandbox_build_index.cpp
c++/sandbox/seqan_sandbox_compile_test.cpp
c++/sandbox/seqan_sandbox_complement.cpp
c++/sandbox/seqan_sandbox_dereference.cpp
c++/sandbox/seqan_sandbox_descend_preferred.cpp
c++/sandbox/seqan_sandbox_global_pos_index.cpp
c++/sandbox/seqan_sandbox_global_pos_range.cpp
c++/sandbox/seqan_sandbox_infix.cpp
c++/sandbox/seqan_sandbox_iterator_const.cpp
c++/sandbox/seqan_sandbox_markov_bg.cpp
c++/sandbox/seqan_sandbox_markov_model.cpp
c++/sandbox/seqan_sandbox_modified_append.cpp
c++/sandbox/seqan_sandbox_n_index.cpp
c++/sandbox/seqan_sandbox_prefix.cpp
c++/sandbox/seqan_sandbox_property.cpp
c++/sandbox/seqan_sandbox_raw_text.cpp
c++/sandbox/seqan_sandbox_rev_comp.cpp
c++/sandbox/seqan_sandbox_rev_comp_iterator.cpp
c++/sandbox/seqan_sandbox_sequence_length.cpp
c++/sandbox/seqan_sandbox_string_set.cpp
c++/sandbox/seqan_sandbox_test_infix.cpp
c++/sandbox/seqan_sandbox_test_link_error.cpp
c++/sandbox/seqan_sandbox_test_log_arithmetic.cpp
c++/sandbox/seqan_sandbox_test_position_storage_speed.cpp
c++/sandbox/seqan_sandbox_test_wmers.cpp
c++/sandbox/seqan_sandbox_top_down_iterator.cpp
c++/sandbox/test-uninit-warning.cpp
c++/sandbox/test_best_w_mer_speed.cpp
c++/sandbox/test_heap.cpp
c++/sandbox/test_int_double_add_speed.cpp
c++/sandbox/vector_mem_usage.cpp
c++/sandbox/multiple_defs/translation_unit_1.cpp
c++/sandbox/multiple_defs/translation_unit_2.cpp
c++/sandbox/test_pvalue_speeds/fast.cpp
c++/sandbox/test_pvalue_speeds/main.cpp
c++/sandbox/test_pvalue_speeds/meme.cpp
c++/sandbox/test_pvalue_speeds/parse.cpp
c++/sandbox/test_pvalue_speeds/pval.cpp
c++/sandbox/test_pvalue_speeds/pvalue_test_defs.h
c++/test/test_bejerano.cpp
c++/test/test_fast.cpp
c++/test/test_hirji_shifted.cpp
c++/test/test_include_background.cpp
c++/test/test_include_binding_model.cpp
c++/test/test_include_data.cpp
c++/test/test_include_defs.cpp
c++/test/test_include_descender.cpp
c++/test/test_include_descender_preferred_order.cpp
c++/test/test_include_em.cpp
c++/test/test_include_find_best_w_mers.cpp
c++/test/test_include_find_instances.cpp
c++/test/test_include_markov.cpp
c++/test/test_include_model.cpp
c++/test/test_include_significance.cpp
c++/test/test_include_start_finder.cpp
c++/test/test_include_steme.cpp
c++/test/test_include_w_mer_evaluation.cpp
c++/test/test_markov_model.cpp
c++/test/test_pvalues.cpp
c++/test/test_segmentize.cpp
c++/test/test_sparse_vector.cpp
c++/test/test_steme_branch_and_bound.cpp
python/STEME.egg-info/PKG-INFO
python/STEME.egg-info/SOURCES.txt
python/STEME.egg-info/dependency_links.txt
python/STEME.egg-info/requires.txt
python/STEME.egg-info/top_level.txt
python/scripts/steme
python/scripts/steme-em
python/scripts/steme-find-spacings
python/scripts/steme-motif-logos
python/scripts/steme-pwm-scan
python/scripts/steme-scan-stats
python/scripts/steme-seqs-2-motif
python/scripts/steme-spacing-analysis
python/scripts/stemewebapp-create-db
python/scripts/stemewebapp-remove-job
python/stemewebapp/INSTALL
python/stemewebapp/STEME.wsgi
python/stemewebapp/__init__.py
python/stemewebapp/application.py
python/stemewebapp/default_settings.py
python/stemewebapp/forms.py
python/stemewebapp/models.py
python/stemewebapp/views.py
python/stemewebapp/static/logo.png
python/stemewebapp/static/logo.svg
python/stemewebapp/static/style.css
python/stemewebapp/templates/_formhelpers.html
python/stemewebapp/templates/home.html
python/stemewebapp/templates/layout.html
python/stemewebapp/templates/listjobs.html
python/stemewebapp/templates/newjob.html
python/stempy/LICENSE
python/stempy/README
python/stempy/VERSION
python/stempy/__init__.py
python/stempy/_html_output.py
python/stempy/_meme_like_output.py
python/stempy/_minimal_meme_output.py
python/stempy/_stempy_build.py
python/stempy/meme.py
python/stempy/meme_parse.py
python/stempy/ntnu.py
python/stempy/planted_sites.py
python/stempy/run_dataset.py
python/stempy/scan.py
python/stempy/spacing.py
python/stempy/test_data.py
python/stempy/tompa.py
python/stempy/_debug_build/__init__.py
python/stempy/_debug_build/_index_genome_wrapper.py
python/stempy/_debug_build/_index_standard_wrapper.py
python/stempy/_release_build/__init__.py
python/stempy/_release_build/_index_genome_wrapper.py
python/stempy/_release_build/_index_standard_wrapper.py
python/stempy/static/style.css
python/stempy/templates/job.html
python/stempy/templates/layout.html
python/stempy/templates/motif.html
python/stempy/templates/options.html
python/stempy/templates/scan-stats.html
python/stempy/templates/wide-layout.html