├── LinearFold ├── .gitattributes ├── AUTHORS ├── LICENSE ├── Makefile ├── README.md ├── draw_circular_plot ├── ecoli_tRNA ├── example.shape ├── gflags.py ├── linearfold ├── old │ ├── Makefile │ ├── gflags.py │ ├── linearfold │ └── src │ │ ├── LinearFold.cpp │ │ ├── LinearFold.h │ │ ├── LinearFoldEval.cpp │ │ └── Utils │ │ ├── energy_parameter.h │ │ ├── feature_weight.h │ │ ├── intl11.h │ │ ├── intl21.h │ │ ├── intl22.h │ │ ├── utility-1.h │ │ ├── utility.h │ │ └── utility_v.h ├── src │ ├── LinearFold.cpp │ ├── LinearFold.h │ ├── LinearFoldEval.h │ ├── Utils │ │ ├── energy_parameter.h │ │ ├── feature_weight.h │ │ ├── intl11.h │ │ ├── intl21.h │ │ ├── intl22.h │ │ ├── shared.h │ │ ├── utility.h │ │ └── utility_v.h │ └── scripts │ │ └── gen_latex_script.py ├── testcons ├── testeval ├── testseq └── vis_examples │ ├── circular_plot.pdf │ └── circular_plot.png ├── README.md ├── RNA-Playground ├── .gitignore ├── Agglomerative-Clustering-120x90.png ├── Agglomerative-Clustering.html ├── Arslan-Egecioglu-Pevzner-120x90.png ├── Arslan-Egecioglu-Pevzner.html ├── Feng-Doolittle-120x90.png ├── Feng-Doolittle.html ├── Gotoh-120x90.png ├── Gotoh-Local-120x90.png ├── Gotoh-Local.html ├── Gotoh.html ├── Hirschberg-120x90.png ├── Hirschberg.html ├── Iterative-Refinement-120x90.png ├── Iterative-Refinement.html ├── MEA-120x90.png ├── MEA-400x300.png ├── MEA.html ├── McCaskill-120x90.png ├── McCaskill-400x300.png ├── McCaskill.html ├── Needleman-Wunsch-120x90.png ├── Needleman-Wunsch.html ├── Notredame-Higgins-Heringa-120x90.png ├── Notredame-Higgins-Heringa.html ├── Nussinov-120x90.png ├── Nussinov-400x300.png ├── Nussinov.html ├── README.md ├── Smith-Waterman-120x90.png ├── Smith-Waterman.html ├── UnitTests.jstd ├── Waterman-Smith-Beyer-120x90.png ├── Waterman-Smith-Beyer.html ├── _config.yml ├── accessibility-120x90.png ├── accessibility-400x300.png ├── accessibility.html ├── alignment.html ├── co-folding-120x90.png ├── co-folding-400x300.png ├── co-folding.html ├── counting-120x90.png ├── counting-400x300.png ├── counting.html ├── css │ ├── dropdown.css │ ├── index.css │ ├── inner_style.css │ └── outer_style.css ├── docs │ ├── Licences.txt │ ├── Presentation.pdf │ ├── ReadMe.txt │ └── unit_test_pdfs │ │ ├── Agglomerative Clustering.pdf │ │ ├── Arslan-Eğecioğlu-Pevzner.pdf │ │ ├── Feng-Doolittle.pdf │ │ ├── Gotoh (Local).pdf │ │ ├── Gotoh, WSB and SoP.pdf │ │ ├── Iterative Refinement.pdf │ │ ├── Needleman-Wunsch & Hirschberg.pdf │ │ ├── Neighbour-Joining.pdf │ │ ├── Notredame-Higgins-Heringa.pdf │ │ ├── Obsolete │ │ ├── Neighbour-Joining.pdf │ │ └── Notredame-Higgins-Heringa.pdf │ │ └── Smith-Waterman.pdf ├── hirschberg_traceback.png ├── hirschberg_traceback.svg ├── hybrid-only-120x90.png ├── hybrid-only-400x300.png ├── hybrid-only.html ├── index.html ├── inner_sprites.png ├── js │ ├── agglomerative_clustering.js │ ├── arslan_egecioglu_pevzner.js │ ├── bases │ │ ├── alignment.js │ │ ├── clustering.js │ │ └── multi_sequence_alignment.js │ ├── defaults.js │ ├── feng_doolittle.js │ ├── formats │ │ ├── csv_parser.js │ │ └── newick_encoder.js │ ├── fornac │ │ ├── css │ │ │ └── fornac.css │ │ └── js │ │ │ ├── FileSaver.js │ │ │ ├── FileSaver.min.js │ │ │ ├── d3.js │ │ │ └── fornac.js │ ├── gotoh.js │ ├── gotoh_local.js │ ├── hirschberg.js │ ├── interfaces │ │ ├── alignment_interface.js │ │ ├── clustering_interface.js │ │ ├── dropdown_menu.js │ │ ├── interface.js │ │ ├── linear_alignment_interface.js │ │ ├── multi_sequence_interface.js │ │ └── subadditive_alignment_interface.js │ ├── iterative_refinement.js │ ├── libs │ │ ├── FileSaver.min.js │ │ ├── d3.min.js │ │ ├── jquery-migrate-1.2.0.min.js │ │ ├── jquery.js │ │ ├── jquery.min.js │ │ ├── jsphylosvg.js │ │ ├── knockout-3.4.0.js │ │ ├── knockout-3.4.2.js │ │ ├── namespace.js │ │ └── raphael-min.js │ ├── loader.js │ ├── needleman_wunsch.js │ ├── neighbour_joining.js │ ├── notredame_higgins_heringa.js │ ├── nussinovmatrix.js │ ├── nussinovmatrix4d.js │ ├── post_processing │ │ ├── input_processor.js │ │ └── visualizer.js │ ├── scripts.js │ ├── smith_waterman.js │ ├── string-format.js │ ├── tests │ │ ├── test_arslan_egecioglu_pevzner.js │ │ ├── test_feng_doolittle.js │ │ ├── test_gotoh.js │ │ ├── test_gotoh_local.js │ │ ├── test_hirschberg.js │ │ ├── test_iterative_refinement.js │ │ ├── test_needleman_wunsch.js │ │ ├── test_neighbour_joining.js │ │ ├── test_notredame_higgins_heringa.js │ │ ├── test_single_linkage.js │ │ ├── test_smith_waterman.js │ │ ├── test_sum_of_pairs.js │ │ ├── test_upgma.js │ │ ├── test_waterman_smith_beyer.js │ │ └── test_wpgma.js │ ├── visualize-forna.js │ ├── visualize.js │ └── waterman_smith_beyer.js ├── logos-src.svg └── outer_sprites.png └── mxfold2 ├── .devcontainer ├── Dockerfile ├── devcontainer.json ├── library-scripts │ ├── common-debian.sh │ ├── node-debian.sh │ └── python-debian.sh └── noop.txt ├── .gitignore ├── .gitmodules ├── .pylintrc ├── LICENSE ├── README.md ├── build.py ├── mxfold2 ├── __init__.py ├── __main__.py ├── 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