My name is Anita Howe. I am a senior scientist at the British Columbia Centre for Disease Control in Canada. I am also the HCV SHARED coordinator, an international collaboration to study HCV drug resistance and transmission.
Thank you for setting up the Nextstrain program. I have downloaded the Zika Tutorial and planned to use it to generate an “HCV Nextstrain”. So far, the display was terrific on my demo set. I have a few questions, and I hope you can help me to understand.
How were the travel lines constructed? Were they primarily based on the sample collection dates, or using both the collection date and the inferred phylogeny?
In the Genotype and the Diversity Pane, does the “Event” mean the number of cases with mutations at each amino acid in the dataset? I suppose the “Entropy” refers to the genetic diversity at each amino acid position.
Because of privacy agreements, we would prefer not to show the individual data; the box appears after clicking the dots in the Phylogeny Pane. Is there possible to turn off the display of some information inside the box, e.g., retain the Gender in the “Color by” on the left panel, but do not show “male” or “female” inside the box?
Lastly, is the phylogenetic tree primarily based on the sequences, or does it also take the sample collection dates into account? Some of our samples do not have detailed dd-mm-yyyy, just the yyyy, and I wonder if I should include these samples in our dataset and how they might affect the phylogeny tree?
Sorry for the long list of questions. I am looking forward to hearing from you, and hopefully, we will have the HCV in your website someday.