├── Docs └── images │ ├── PDF_icon.svg │ ├── Simplot_ex_clipped.svg │ ├── Simplot_ex_svg.svg │ ├── User_preferences.png │ ├── bootscan_gif.gif │ ├── findsite.gif │ ├── group_page_steps.png │ ├── group_page_steps_gif.gif │ ├── newtwork_gif.gif │ ├── plot_toolbar.gif │ ├── recomb_gif.gif │ └── simplot_gif.gif ├── LICENSE ├── PyQt5_gui ├── PyQT5_project │ ├── app_settings.ui │ ├── bootscan_dialog.ui │ ├── file_info_dialog.ui │ ├── group_list_widget.ui │ ├── gui_test.pro │ ├── gui_test.pro.user │ ├── gui_test.pro.user.4a7d66f │ ├── gui_test.pro.user.6d2e820 │ ├── icons │ │ ├── Icons.qrc │ │ ├── active │ │ │ ├── Bootscan_page_active.svg │ │ │ ├── View_new_window_active.svg │ │ │ ├── browse_active.svg │ │ │ ├── findsite_page_active.svg │ │ │ ├── group_page_active.svg │ │ │ ├── launch_active.svg │ │ │ ├── network_page_active.svg │ │ │ ├── pause_button.svg │ │ │ ├── question_active.svg │ │ │ ├── recombination_active.svg │ │ │ ├── reopen_active.svg │ │ │ ├── save_groups_active.svg │ │ │ ├── save_html_active.svg │ │ │ ├── save_text_active.svg │ │ │ ├── settings_active.svg │ │ │ ├── simplot_page_active.svg │ │ │ ├── user_pref_active.svg │ │ │ └── view_quality_active.svg │ │ ├── csv_button.svg │ │ ├── detectiom.svg │ │ ├── detection.svg │ │ ├── disabled │ │ │ ├── Bootscan_page_grey.svg │ │ │ ├── View_new_window_disabled.svg │ │ │ ├── browse_grey.svg │ │ │ ├── findsite_page_grey.svg │ │ │ ├── group_page_grey.svg │ │ │ ├── launch_disabled.svg │ │ │ ├── network_page_grey.svg │ │ │ ├── recombination_disabled.svg │ │ │ ├── reopen_grey.svg │ │ │ ├── save_groups_grey.svg │ │ │ ├── save_html_disabled.svg │ │ │ ├── save_text_disabled.svg │ │ │ ├── settings_disabled.svg │ │ │ ├── simplot_page_grey.svg │ │ │ ├── user_pref_disabled.svg │ │ │ └── view_quality_disabled.svg │ │ ├── hover │ │ │ ├── Bootscan_page_hover.svg │ │ │ ├── View_new_window_hover.svg │ │ │ ├── browse_hover.svg │ │ │ ├── findsite_page_hover.svg │ │ │ ├── group_page_hover.svg │ │ │ ├── launch_hover.svg │ │ │ ├── network_page_hover.svg │ │ │ ├── question_hover.svg │ │ │ ├── recombination_hover.svg │ │ │ ├── reopen_hover.svg │ │ │ ├── save_groups_hover.svg │ │ │ ├── save_html_hover.svg │ │ │ ├── save_text_hover.svg │ │ │ ├── settings_hover.svg │ │ │ ├── simplot_page_hover.svg │ │ │ ├── user_pref_hover.svg │ │ │ └── view_quality_hover.svg │ │ ├── icons_rc │ │ ├── icons_rc.py │ │ ├── logo │ │ │ └── simplot++_logo.svg │ │ ├── other │ │ │ ├── Method Draw Vector Editor_files │ │ │ │ ├── all.css │ │ │ │ └── all.js.download │ │ │ ├── chevron-down.svg │ │ │ ├── chevron-up.svg │ │ │ ├── delete.svg │ │ │ ├── dna.svg │ │ │ ├── down_arrow.svg │ │ │ ├── edit.svg │ │ │ └── up-arrow.svg │ │ ├── pause_button.svg │ │ └── pressed │ │ │ ├── Bootscan_page_pressed.svg │ │ │ ├── View_new_window_pressed.svg │ │ │ ├── browse_pressed.svg │ │ │ ├── findsite_page_pressed.svg │ │ │ ├── group_page_pressed.svg │ │ │ ├── launch_pressed.svg │ │ │ ├── network_page_pressed.svg │ │ │ ├── question_pressed.svg │ │ │ ├── recombination_pressed.svg │ │ │ ├── reopen_pressed.svg │ │ │ ├── save_groups_pressed.svg │ │ │ ├── save_html_pressed.svg │ │ │ ├── save_text_pressed.svg │ │ │ ├── settings_pressed.svg │ │ │ ├── simplot_page_pressed.svg │ │ │ ├── user_pref_pressed.svg │ │ │ └── view_quality_pressed.svg │ ├── main.cpp │ ├── mainwindow.cpp │ ├── mainwindow.h │ ├── mainwindow.ui │ ├── model_dialog.cpp │ ├── model_dialog.h │ ├── model_dialog.ui │ ├── seq_window.cpp │ ├── seq_window.h │ ├── seq_window.ui │ ├── simplot_settings_form.cpp │ ├── simplot_settings_form.h │ └── simplot_settings_form.ui ├── __init__.py ├── app_settings.py ├── bootscan_dialog.py ├── build-gui_test-Desktop_Qt_5_15_1_MinGW_32_bit-Debug │ ├── .qmake.stash │ ├── Makefile │ ├── Makefile.Debug │ ├── Makefile.Release │ ├── debug │ │ ├── main.o │ │ ├── mainwindow.o │ │ ├── moc_mainwindow.cpp │ │ ├── moc_model_dialog.cpp │ │ ├── moc_model_dialog.o │ │ ├── moc_predefs.h │ │ ├── moc_seq_window.cpp │ │ ├── moc_seq_window.o │ │ ├── model_dialog.o │ │ └── seq_window.o │ ├── ui_bootscan_dialog.h │ ├── ui_file_info_dialog.h │ ├── ui_mainwindow.h │ ├── ui_model_dialog.h │ └── ui_seq_window.h ├── file_info_dialog.py ├── group_list_widget.py ├── group_widget.py ├── group_widget_info.txt ├── model_dialog.py ├── seq_window.py ├── simplot_settings_form.py └── ui_main.py ├── README.md ├── SimPlot.ico ├── example_data ├── HIVULN_groups.nexus ├── h_pylori.fasta ├── sars_cov_2_gene_s.fas └── sars_cov_2_gene_s_grouped.nexus ├── lib ├── Bootscan │ └── bootscan.py ├── DistanceModels │ └── DistCalc.py ├── FindSites │ └── findsites.py ├── Misc │ ├── RGB_colors.py │ ├── global_running.py │ ├── groups_class.py │ └── preferences.py ├── Network │ ├── Bokeh_graph_functions.py │ ├── network_analysis.py │ └── recombination_detection.py ├── SimPlot │ ├── analysis_class.py │ └── quality_report.py └── recombination_tests │ ├── lib │ ├── misc.py │ ├── pair_score.py │ ├── queue.py │ ├── seq_manip.py │ └── stats.py │ └── phipack_main.py ├── main.py ├── 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