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Running beast for the first time this tutorial will guide you through running beast and some of its accessory programs to do a simple phylogenetic analysis The summary information includes the posterior probabilities of the nodes in the target tree, the posterior estimates and hpd limits of the node heights and (in the case of a relaxed molecular clock model) the rates. If you haven’t already, download and install beast following these instructions.
Figtree is a program for viewing trees, including summary information produced by treeannotator, and producing publication quality figures. Treeannotator is a program to summarize the information from a sample of trees produced by beast onto a single “target” tree Beast | bayesian evolutionary analysis sampling trees
This is the main program that takes a control file generated by beauti and performs the analysis.
The current version of beagle will only work with beast v1.6 or later downloading and installing beagle. 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 Installing beast beast has been developed in java, which allows the same code to run on any platform that has the java software installed
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