about.md

How datelife works

Datelife the R package

https://github.com/phylotastic/datelife

Goals

• Users give input
  • List of names
  • Topology
  • Tree with branch lengths
  • in all cases names can correspond to species or higher-taxon names
• They get back one of
  • A single chronogram
    • With matching taxa only (done)
    • With all taxa (ish)
  • The depth of the split
  • A patristic distance matrix
• Or any of the above, but one per reference tree rather than an aggregate
• There are also relatively untested approaches to use, like using BOLD or supertrees

Technologies

• R, rotl, geiger, ape packages

Datelife.org the website

• Server is omearalab19 in my lab. Currently dedicated to this. Trash can Mac Pro.
• A dockerfile (https://github.com/phylotastic/datelifedocker) is used to set up the server. See its readme for how to do this, as well as the contents of the Dockerfile itself.
• The website itself (https://github.com/phylotastic/datelifeweb) is a mixture of HTML and R Shiny
• The query and citations directories contain different Shiny apps.