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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 considers the present or most recent sampling time as time 0). 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
If you haven’t already, download and install beast following these instructions. The sequences are assumed to be sampled at the same time Beast | bayesian evolutionary analysis sampling trees
This is the main program that takes a control file generated by beauti and performs the analysis.
Figtree is a program for viewing trees, including summary information produced by treeannotator, and producing publication quality figures. Installing beast beast has been developed in java, which allows the same code to run on any platform that has the java software installed The current version of beagle will only work with beast v1.6 or later downloading and installing beagle. To inform beauti/beast about the sampling dates of the sequences, go to the tips menu and select the “use tip dates” option
By default all the taxa are assumed to have a date of zero (i.e
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