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lines changed- 229e_after2009
- .ipynb_checkpoints
- auspice
- config
- data
- results
- 229e
- auspice
- config
- data
- results
- all_hcovs
- 1000nt_filter
- auspice
- results
- auspice
- config
- data
- results
- starter_data
- antigenic_evolution
- .ipynb_checkpoints
- bhatt_config
- bhatt_results_nextstrain_old
- flu_12y
- bhatt_results_nextstrain
- bhatt_results_old
- simulated
- bhatt_results
- simulated
- pact
- 229e
- 229e_envelope
- 229e_membrane
- 229e_nucleocapsid
- 229e_rdrp
- 229e_replicase1ab
- 229e_s1
- 229e_s2
- 229e_spike
- hku1A
- hku1A_envelope
- hku1A_membrane
- hku1A_nucleocapsid
- hku1A_rdrp
- hku1A_replicase1ab
- hku1A_s1
- hku1A_s2
- hku1A_spike
- hku1B
- hku1B_envelope
- hku1B_membrane
- hku1B_nucleocapsid
- hku1B_rdrp
- hku1B_replicase1ab
- hku1B_s1
- hku1B_s2
- hku1B_spike
- nl63
- nl63_envelope
- nl63_membrane
- nl63_nucleocapsid
- nl63_rdrp
- nl63_replicase1ab
- nl63_s1
- nl63_s2
- nl63_spike
- oc43A
- oc43A_envelope
- oc43A_membrane
- oc43A_nucleocapsid
- oc43A_rdrp
- oc43A_replicase1ab
- oc43A_s1
- oc43A_s2
- oc43A_spike
- oc43B
- oc43B_envelope
- oc43B_membrane
- oc43B_nucleocapsid
- oc43B_rdrp
- oc43B_replicase1ab
- oc43B_s1
- oc43B_s2
- oc43B_spike
- plots
- auspice
- beast
- 229e
- rdrp
- s1
- s2
- spike
- hku1a
- rdrp
- s1
- s2
- spike
- hku1b
- rdrp
- s1
- s2
- spike
- hku1
- rdrp
- s1
- s2
- spike
- nl63
- rdrp
- s1
- s2
- spike
- oc43a
- rdrp
- s1
- s2
- spike
- oc43b
- rdrp
- s1
- s2
- spike
- oc43
- rdrp
- s1
- s2
- spike
- data-wrangling
- .ipynb_checkpoints
- hku1
- auspice
- config
- data
- results
- manuscript
- corrections
- manuscript_pdfs
- old
- figure_components