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Figtree is a program for viewing trees, including summary information produced by treeannotator, and producing publication quality figures. 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 The current version of beagle will only work with beast v1.6 or later downloading and installing beagle.
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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 Tracer v1.7.2 can read output files from mrbayes, beast, beast2, revbayes. If you haven’t already, download and install beast following these instructions.
Installing beast beast has been developed in java, which allows the same code to run on any platform that has the java software installed
Treeannotator is a program to summarize the information from a sample of trees produced by beast onto a single “target” tree 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. Tracer (now at version 1.7.2) is a software package for visualising and analysing the mcmc trace files generated through bayesian phylogenetic inference Tracer provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more
