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The second step is to actually run BEAST using the input file that contains the data, model and settings.

1 The final step is to explore the output of BEAST in order to diagnose problems and to summarize the results.

Relaxed Phylogenetics and Dating with Confidence Alexei J Drummond, Andrew Rambaut and Walter Xie February 10, 2012 Introduction This practical will introduce the BEAST software for Bayesian evolutionary analysis, with a focus on estimating phylogenies and divergence times when you have calibration information from fossil evidence or other prior knowledge.

You will need the following software at your disposal: • BEAST - this package contains the BEAST program, BEAUti, Tree Annotator and other utility programs.

The goal is to estimate the phylogeny as well as the rate of evolution on each lineage based on dates of divergence of their host species.

The first step will be to convert a NEXUS file with a DATA or CHARACTERS block into a BEAST XML input file.

W.; Phillips, Matthew J.; Rambaut, Andrew In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum.

From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

In the next table along you will see the available taxa. Now repeat the whole procedure creating a set called Human-Chimp that contains only Homo sapiens and Pan taxa. Unlink partition models At this point we will need to unlink the substitution model so that each parameter is estimated separately for the two partitions.

The screen should look like this: 3 Finally, create a taxon group that contains everything under the hominoid/cercopithecoid split (i.e. To do this return to Data Partitions panel, select both partitions in the table and click the Unlink Subst Models button.

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum.

These models open the gate to a new field of ‘‘relaxed phylogenetics.’’ Here we introduce a new approach to performing relaxed phylogenetic analysis.

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