don86 / dengue-in-data Goto Github PK

• used cd-hit to reduce those with > 300 records in a country, with -i 1. Final: 10,821 tips
• Tree computed with fasttree v2.1.8

Uses http-server for a local server. To install:

npm install http-server -g

To run:

http-server

• A chloropleth (i.e. "map") visualization about the persistence patterns of dengue. If dengue is animal-borne, and has rate of mutation within a certain range, is this reasonable explanation for geographic clustering (as opposed to flu B, which is just everywhere)?
• A treetime computed tree. Unlike certain phylogenetic models (SIR, if I'm not wrong), though, the internal nodes in this case are not the unsampled individuals. As such, I'm still not comfortable with interpreting the vanilla phylogenetic tree as anything more than a dendrogram - I see phrases like "ancestral structure and relationships" all the time, but this (a) doesn't actually mean anything and (b) suffers from Cubist Chicken syndrome.