Divergence Time Estimation using BEAST

A guided tutorial on Bayesian inference of species divergence times

**** This tutorial was written for BEAST v2.4.2***

Instructions are provided in a step-by-step tutorial

Download the data and output files:

The exercises require that you have the following software programs:

  • BEAST v2  (includes BEAST, BEAUti, LogCombiner, & TreeAnnotator)
    • When you install and run BEAST v2, open the BEAUti tool within the provided binaries and install the “SA” package in the file menu: File->Manage Packages. Then click on the SA package in the list and Install/Upgrade. Once you have done this, RESTART BEAUti to complete the installation.
  • FigTree
  • Tracer
  • R

Lecture Slides

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Creative Commons License This tutorial was written by Tracy Heath for workshops on applied phylogenetics and molecular evolution and is licensed under a Creative Commons Attribution 4.0 International License. Source URL: http://treethinkers.org/divergence-time-estimation-using-beast/.

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Outdated Tutorial PDFs:

8 thoughts on “Divergence Time Estimation using BEAST

  1. Evan

    Hey, I’m trying to go through this tutorial and I’ve noticed that the divtime_start_tree.tre is missing from the data.zip file. Am I missing something?

    Reply
    1. Tracy Heath Post author

      You do not need a starting tree for the current version of this tutorial (BEAST v2.*). That was for the outdated version in BEAST v1.7.5. I only leave the old tutorial PDF here and not all of the associated data and output files. If you really want to use that tutorial, you should build a starting tree and make sure that it is consistent with your priors.

      Reply
  2. mark miller

    Hi,
    I downloaded the presentation from SlideShare. It is fabulous, thanks for posting it. But unfortunately, the download version ends at slide 102. Also I had trouble scrolling though the slides embedded in the web page here. It seems you reach about 85 or 86, and it jumps right back to 79. This was a consistent behavior.

    Mark

    Reply
    1. mark miller

      A couple of other comments:
      Using BEAUTI on windows, I found that checking and unchecking Link Site Models as suggested in the tutorial caused the .xml file to be non-functional, and it broke the ability of the interface to link and unlink site models, clock models, and trees. If I configured site models individually without linking them, there was no issue.

      Second, Figure 19 is incorrect. It represents the values if Offset is 20, not 40 as indicted in the instructions.
      It doesn’t matter for the exercise, but just wanted o flag it.

      Reply
  3. Ginsea Chen

    Dear Dr.
    Thanks for your tutorial about beast software, which have been a hand book for my beast learning. Now I have a problem in Figure 16. I have no find Fossilized Birth Death Model in option of Tree prior although I have done all setting as your description. Now I don’t know how to solve it, please help me. My Beast version is 2.2.1.
    Thanks for your help!
    Best Regards!
    Yours.

    Reply
    1. Tracy Heath Post author

      Hi. You need to install the “SA” plug-in in the BEAST 2 package manager. This is described in section 4.2.1 of the tutorial PDF. If you have already done that, you probably have to restart BEAUti before the package is fully installed.

      Reply
  4. Diego

    Hi Tracy, I found your tutorials an excellent way to learn and apply concepts underlying BEAST. I am interested in using the files corresponding to a previous version of your tutorial entitled: Divergence Time Estimation using BEAST v2.1.3

    I find the files are different from the actual tutorial, and would appreciate if you could send them to me via email (or tell me if there is a site where the are hosted).

    Best wishes,

    Diego

    Reply
  5. Xiao Ding

    Hi~
    This is a excellent tutorial of Beast2, cause the Beast 2 is a hard-to-use tool for new researcher, just as me. Well, I has a very basic question for the Beast, is that, what is the role of the tips dates for the samples used in Beast? Will be have some effects for the phylogenetic analysis if I don’t use the tips. Another question, how can I set the tip to month for the sample? For example, the collection date of sample A is Jan 2009,and what should I write in the data blank of this sample? Thank you very much! Hope you can kindly help me.
    Best!

    Reply

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