Dr. Nate Samuels
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BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without ...
Jun 17, 2016 · Download BEAST v1.8.4 binaries for Mac, Windows and UNIX/Linux. Version 1.8.4 released 17th June 2016. New Features: New structured list of citations printed to screen before running. Option ('-citation_file') to write citation list to file. Option in BEAUti Priors panel to set parameters to 'Fixed Value'.
First Tutorial. An introductory tutorial to getting started with BEAST. This tutorial describes the use of BEAUti and BEAST to analyse some primate sequences and estimate a phylogenetic tree. It will take you through the process of importing an alignment, making choices about the model, generating a BEAST XML file. You will then run BEAST.
BEAUti is a graphical user-interface (GUI) application for generating BEAST XML files. It is distributed in the same package as BEAST. To download it, go to the BEAST download page. Run BEAUti by double-clicking on the BEAUti icon in the package you downloaded. See here for a guide to using BEAUti to create BEAST input XML. ©2024 BEAST Developers.
Downloading and running BEAST on Linux. Start by downloading and unpacking the compressed .tar.gz file: tar -zxvf BEASTv10.5.0-beta4.tgz. You can now go to the /bin directory and run BEAUti and BEAST from this directory: cd BEASTv10.5.0-beta4/bin. ./beauti.
Tracer. Tracer is a graphical tool for visualization and diagnostics of MCMC output. 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 ...
Features. Cross-platform graphical tree display. Three different tree styles: rectangular, polar and radial. Display of node heights, branch lengths, support values and other annotations. Node height range bars if available. Collapse of clades into triangles. Colouring of branches and tip labels. Colouring by annotation (for example, support ...
Installing BEAST. BEAST has been developed in Java, which allows the same code to run on any platform that has the Java software installed. We have also created packages for each of the common operating systems to provide a user-interface that is ‘native’ and familiar.
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics package. It can make use of highly-parallel processors such as those in graphics processing units (GPUs) found in many PCs. The current version of BEAGLE will only work with BEAST v1.6 or later.
The aim of this tutorial is to estimate the ancestral locations of the virus using a Bayesian discrete phylogeographic approach and, at the same time, infer the history of host jumping using the same model approach. Using an extension of the discrete diffusion model, we will then test the factors that underly the host transition dynamics.
