├── .gitignore ├── README.md ├── data ├── ebola │ ├── ebola.fasta │ ├── ebola.metadata.csv │ └── ebola.nwk ├── h3n2_na │ ├── h3n2_na_20.fasta │ ├── h3n2_na_20.metadata.csv │ ├── h3n2_na_20.nex │ ├── h3n2_na_20.nwk │ ├── h3n2_na_20.phylip │ ├── h3n2_na_200.fasta │ ├── h3n2_na_200.metadata.csv │ ├── h3n2_na_200.nwk │ ├── h3n2_na_20_aa.fasta │ ├── h3n2_na_500.fasta │ ├── h3n2_na_500.metadata.csv │ └── h3n2_na_500.nwk ├── tb │ ├── lee_2015.informative_sites.fasta │ ├── lee_2015.metadata.tsv │ ├── lee_2015.nwk │ ├── lee_2015.vcf.gz │ └── tb_ref.fasta └── zika │ ├── zika.country_weights.csv │ ├── zika.fasta │ ├── zika.metadata.csv │ ├── zika.nwk │ └── zika.phylip ├── figures ├── clock_plot.png ├── ebola_outliers.png ├── ebola_skyline.png ├── timetree.png └── tree_and_clock.png └── scripts ├── ancestral_sequence_inference.py ├── ebola.py ├── relaxed_clock.py └── rerooting_and_timetrees.py /.gitignore: -------------------------------------------------------------------------------- 1 | 201* 2 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