├── .gitattributes ├── .gitignore ├── .gitlab-ci.yml ├── LICENSE ├── README.md ├── SPR_analysis.md ├── acknowledgements ├── README.md ├── gisaid_hcov-19_acknowledgement_pre_June19th.tsv ├── gisaid_hcov-19_acknowledgement_table_2020-06-19_to_2020-07-02.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-07-02_to_2020-07-12.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-07-12_to_2020-07-24.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-07-24_to_2020-07-31.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-07-31_to_2020-08-07.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-08-07_to_2020-08-14.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-08-14_to_2020-08-21.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-08-21_to_2020-08-28.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-08-28_to_2020-09-11.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-09-11_to_2020-09-18.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-09-18_to_2020-09-25.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-09-25_to_2020-09-27.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-09-28_to_2020-09-28.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-09-29_to_2020-10-04.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-10-05_to_2020-10-14.pdf ├── gisaid_hcov-19_acknowledgement_table_2020-10-15_to_2020-10-21.pdf └── gisaid_hcov-19_acknowledgement_table_2020-10-22_to_2020-10-26.pdf ├── ci └── Dockerfile ├── environment.yml ├── excluded_sequences.tsv ├── fasttreeOMP.md ├── ftOMP.xlsx ├── ft_SH.tree ├── ft_models.xlsx ├── iqtree_sequential.md ├── iqtree_vs_fasttree.md ├── model_selection_results.csv ├── onlinephylo.md ├── onlinephylo.xlsx ├── scripts ├── QC.R ├── add_seqs_to_global_tree.sh ├── add_seqs_to_tree.sh ├── clean_gisaid.sh ├── clean_tree.R ├── filter_aln.sh ├── global_profile_alignment.sh ├── global_tree_gisaid.sh ├── global_tree_gisaid_start_tree.sh ├── lsd2.sh ├── mask_alignment.sh ├── mask_seq.py └── update_excluded_seqs.R ├── 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