Bayesian Phylogenetic Analysis with BEAST 2.06: A Tutorial

Beast 2.06 Software Download: A Guide for Bayesian Phylogenetic Analysis

If you are interested in Bayesian phylogenetic analysis of molecular sequences, you may have heard of beast 2.06 software. This is a cross-platform program that allows you to estimate rooted, time-measured phylogenies using various models and methods. It can also be used as a framework for testing evolutionary hypotheses without conditioning on a single tree topology.

Beast 2.06 software is a rewrite of beast 1.x, which has been widely used by researchers for over a decade. Beast 2.06 software has a greater emphasis on modularity, which makes it easier to extend and customize via its package system. As a result, beast 2.06 software has rapidly acquired the ability to perform a diverse array of model-based analyses, such as species tree inference, gene tree reconciliation, ancestral sequence reconstruction, molecular dating, biogeography, epidemiology, and more.

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In this article, we will guide you through the process of downloading, installing, and using beast 2.06 software for your phylogenetic analysis. We will also provide some tips and resources for further learning and support.

How to Download and Install Beast 2.06 Software

The first step is to download the latest version of beast 2.06 software for your operating system. You can find the download links on the official website: [1]( The current version is beast v2.7.4, which was released on October 14th, 2021.

Depending on your operating system, you can choose one of the following options:

• Download for Windows (90MB)

• Download for Mac OS X (87MB)

• Download for Linux x86 (91MB) / aarch64 (92MB)

After downloading the installer, you need to run it and follow the instructions on the screen. The installer will create a folder called BEAST v2.X.X in your chosen location, which contains all the necessary files and programs for running beast 2.06 software.

How to Use Beast 2.06 Software

To use beast 2.06 software, you need to perform three main steps:

• Set up the analysis and generate the XML file using BEAUti

• Run the analysis and sample from the posterior distribution using BEAST

• Visualize and interpret the results using Tracer, FigTree, and other programs

How to Set Up the Analysis and Generate the XML File Using BEAUti

BEAUti is a graphical user interface program that allows you to set up your analysis and generate the XML file that contains all the information needed by BEAST. You can find BEAUti in the BEAST v2.X.XBEAUti has a menu bar and a tabbed panel that allow you to navigate through different options and settings. You can also use the Help menu to access the online documentation and tutorials.

The first thing you need to do is to load your molecular sequence data into BEAUti. You can do this by clicking on the File menu and selecting Import Alignment. You can then browse your computer and select the file that contains your sequence data. BEAUti supports various file formats, such as FASTA, NEXUS, PHYLIP, and XML.

After loading your data, you will see a table that shows the name, type, and length of each partition. A partition is a subset of your data that can have different models and parameters. For example, you can partition your data by gene, codon position, or locus. You can also merge or split partitions by using the buttons at the bottom of the table.

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The next step is to specify the models and priors for each partition. You can do this by clicking on the tabs on the left panel. For example, you can click on the Site Model tab to choose the substitution model, the rate heterogeneity model, the proportion of invariant sites, and the base frequencies for each partition. You can also click on the Clock Model tab to choose the molecular clock model, such as strict, relaxed, or random local clock. You can also click on the Prior tab to specify the prior distributions for each parameter, such as the tree height, the branch rates, the substitution rates, and the population sizes.

The last step is to specify the MCMC options for your analysis. You can do this by clicking on the MCMC tab on the left panel. Here you can set the chain length, the sampling frequency, the file names, and other options for running BEAST. You can also click on the Operators tab to see and modify the operators that are used to propose new states in the MCMC chain.

Once you have finished setting up your analysis, you can save your XML file by clicking on the File menu and selecting Save or Save As. You can also validate your XML file by clicking on the File menu and selecting Validate. This will check if your XML file is well-formed and consistent with the beast 2.06 software schema.

How to Run the Analysis and Sample from the Posterior Distribution Using BEAST

BEAST is a command-line program that runs your analysis and samples from the posterior distribution of trees and parameters. You can find BEAST in the BEAST v2.X.X folder that was created by the installer.

To run BEAST, you need to open a terminal or a command prompt window and navigate to the folder that contains your XML file. Then you need to type the following command:

beast -beagle -seed 12345 -overwrite -working my_analysis.xml

This command will run BEAST with some options that are recommended for most analyses:

• -beagle: This option will use the BEAGLE library, which is a high-performance computing library that can speed up your analysis by using GPUs or CPUs.

• -seed 12345: This option will set the random number seed to 12345, which is useful for reproducibility. You can change this number to any integer value.

• -overwrite: This option will overwrite any existing output files with the same name as your XML file.

• -working: This option will save all output files in the same folder as your XML file.

• my_analysis.xml: This is the name of your XML file that contains all the information for your analysis.

You can also use other options that are available in BEAST by typing beast -help. For example, you can use -threads X to specify how many threads (cores) you want to use for your analysis.

When you run BEAST, you will see some messages on your terminal or command prompt window that show the progress of your analysis. You will also see some output files that are generated by BEAST in your working folder. These files include:

• my_analysis.log: This file contains a log of various parameters and statistics that are sampled from the posterior distribution every X iterations, where X is the sampling frequency that you specified in BEAUti. You can use Tracer to visualize and analyze this file.

• my_analysis.trees: This file contains a sample of trees from the posterior distribution every X iterations, where X is the sampling frequency that you specified in BEAUti. You can use FigTree or other programs to visualize and summarize this file.

my_analysis.xml.state: This file contains th