Peter Beerli's Classes

Beast SNAPP tutorial

Tutorial: The tutorial follows roughtly the SNAPPtutorial.pdf I added an additional tutorial (BFDtutorial.pdf) which we will not tackle, but if you multiple populations and want to delineate species you may want to check it out. We use the same data set hemi129.nex for our SNAPPtutorial.pdf; there is a map of the distribution of the species in the BFDtutorial.pdf.

rough guide:

install snapp following the SNAPPtutorial.pdf

try to set up the run with Beauti

run

use tracer to look at convergence

use a tree viewer program (e.g. diversitree, figtree) to look at output trees

use treeannotator to extract the maximum posterior tree.

Installation issues

• if you have the wrong Java version [you need 1.8]

• download the 1.8 runtime java version (on macs you should have automatically the last version; on windows you may need to download, but there may be a windows installer; on linux: go to oracle's website and download a package like jre-8u65-linux-x64.tar.gz ), unpack it and move to a place you can access then change your .bash_profile so that

  export JAVAPATH=/path/to/the/jre/directory # you need to give here the path you have export
  PATH=$JAVAPATH/bin:$PATH
  

  make sure not have typos on these lines because, if you fail to have a path recovery is awkard on the classroom machines you need to execute the commands in the terminal you want to use to start beauti and beast:

  export JAVAPATH=/research/pbeerli/javastuff/jre1.8.0_65 
  export PATH=$JAVAPATH/bin:$PATH # after that you can run 
  /research/pbeerli/bin/beast2.3.1/bin/beauti
  

• if you cannot find the SNAPP directory and are on
• mac and cannot find the the SNAPP directory: look in ~/Library/Application Support/Beast

• linux and cannot find the the SNAPP directory: look in ~/.beast [beauti shows the path to the directory in the window title]

• if beauti does not show templates and working directories, the you you will need to get the beauti and beast from the new beast version 2 (beast2.org) and not beast 1.8.