It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.Bayesian inference refers to a probabilistic method developed by Reverend Thomas Bayes based on Bayes' theorem.Published posthumously in 1763 it was the first expression of inverse probability and the basis of Bayesian inference.The goal is to estimate the phylogeny, the rate of evolution on each lineage and the ages of the uncalibrated ancestral divergences.
The molecular clock was first tested in 1962 on the haemoglobin protein variants of various animals, and is commonly used in molecular evolution to estimate times of speciation or radiation.
The second step is to actually run BEAST using the input file generated by BEAUTi, which contains the data, model and analysis settings.
The final step is to explore the output of BEAST in order to diagnose problems and to summarize the results.
The tutorial involves co-estimation of a gene phylogeny and associated divergence times in the presence of calibration information from fossil evidence.
You will need the following software at your disposal: This tutorial will guide you through the analysis of an alignment of sequences sampled from twelve primate species (see Figure 1).
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