.
├── raw_data
│ ├── COVID-19-data-linked - Shortcut.lnk
│ └── gisaid_cov2020_sequences.fasta
├── src
│ ├── Preprocessing.ipynb
│ ├── bubbleTree.py
│ ├── circularTree.py
│ ├── compareTree.py
│ ├── nodeStyle.py
│ ├── nodeStyleColored.py
│ ├── plainTree.py
│ ├── semi_tree.pdf
│ ├── treeDrawingEngine.py
│ └── treeInTree.py
└── trees
├── gisaid_cov2020_sequences_filtered_8312_age.nwk
└── gisaid_cov2020_sequences_filtered_8312_age_country.nwk
Notes: raw_data directory is git-ignored
pip3 install -r requirements.txt
From Raw Data (GISAID fasta and nextstrain metadata), you can use Preprocessing.ipynb to filter out those useful data. In this case, we set it to host: human with known age, gender, country, and submitted date
Raw data from GISAID: https://www.epicov.org/epi3/frontend#61101
Nextstrain GISAID metadata: https://github.com/nextstrain/ncov
Nextstrain GISAID metadata is now avalable on GISAID: more instruction here