├── .circleci └── config.yml ├── .gitattributes ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── binder ├── environment.yml └── postBuild ├── conftest.py ├── devtools ├── conda-recipe │ └── meta.yaml ├── create_bibliography_nb.py └── install_miniconda.sh ├── manuscript ├── .gitignore ├── README.md ├── figures │ ├── figure_1.pdf │ ├── figure_2.pdf │ ├── figure_3.pdf │ ├── figure_4.pdf │ ├── figure_5.pdf │ ├── figure_6.pdf │ ├── figure_7.pdf │ ├── tutorials-logo.png │ └── workflowchart.svg ├── literature.bib ├── livecoms.cls ├── manuscript.tex └── vancouver-livecoms.bst ├── notebooks ├── .gitignore ├── 00-pentapeptide-showcase.ipynb ├── 01-data-io-and-featurization.ipynb ├── 02-dimension-reduction-and-discretization.ipynb ├── 03-msm-estimation-and-validation.ipynb ├── 04-msm-analysis.ipynb ├── 05-pcca-tpt.ipynb ├── 06-expectations-and-observables.ipynb ├── 07-hidden-markov-state-models.ipynb ├── 08-common-problems.ipynb └── static │ ├── hmm-backbone-1-385x432.png │ ├── 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