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Phyletica

Exploring biodiversification.

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We are looking forward to the comparative phylogeography workshop at the SSB meeting in Columbus, Ohio. If you are participating, before the workshop, please try installing the software that we will be using. This will allow us to cover more interesting material during our time together and will lessen our reliance on guest WiFi. Instructions for installing the software are here:

http://phyletica.org/ecoevolity/installation.html

Please install ecoevolity and pycoevolity, the R packages used by pycoevolity, and the example data (this is all explained at the link). Either direct installation or getting the Docker image is fine (also explained at the link). Also, though not required, I recommend you also install Tracer for visualizing MCMC chain output from ecoevolity:

http://tree.bio.ed.ac.uk/software/tracer/

You will also need a plain text editor; Sublime Text (http://www.sublimetext.com/) is a nice example.

Lastly, it might be helpful to read the preprint that describes the method implemented in ecoevolity (https://www.biorxiv.org/content/early/2018/05/17/324525). We will cover some of the theory behind the method at the beginning of the workshop, but having some context will likely help.

If you run into trouble installing ecoevolity and/or pycoevolity, please use the community forum to seek help:

https://groups.google.com/forum/#!forum/ecoevolity-users

Thank you for your help with making the workshop run smoothly. See you in Columbus!