Beast2 is a software for co-estimating phylognetic trees and divergence times. During this project, we’re going to be generating a lot of BEAST2 files as we add data and explore data subsampling. Beast2 has some challenging facets, such as that all your taxa must be present in all of your data subsets. For my data, this means all my taxa that have morphological data need to be present in the molecular partition (with question marks as data) and vice versa.

Assembling those datasets by hand can be really tricky, and most tutorials on using BEAST2 start from the assumption that you’ve already done this step. I’ve uploaded two iPython notebooks that take you through the process of crunching and combining data. The first covers assembling all the data into one Beast file. The second covers subsampling the fossil data and making Beast files from a subset of the data. iPython notebooks don’t render well in Github, so you’ll have to download the repository to play with them.

Hopefully these notebooks are helpful for those of you who do combined molecular-morphological analyses in BEAST2. If you’re interested in how I organized the data to be able to do this data crunching so quickly, see here.