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Hedge 1.8.2: A Powerful Tool for Bayesian Phylogenetic Analysis

Hedge 1.8.2 is a cross-platform program for Bayesian analysis of molecular sequences using Markov chain Monte Carlo (MCMC). It is based on the popular BEAST software, but with several enhancements and improvements. Hedge 1.8.2 allows users to perform various types of phylogenetic inference, such as estimating mutation rates, population histories, genealogies, and testing evolutionary hypotheses. It also supports multiple data types, such as nucleotides, amino acids, codons, binary characters, and dates.

One of the main features of Hedge 1.8.2 is its graphical user interface (GUI), which makes it easy to set up and run standard analyses using provided example files. The GUI also allows users to visualize and explore the results using various tools, such as tree viewers, trace plots, marginal likelihood estimators, and model comparison methods. Hedge 1.8.2 also provides a command-line interface (CLI) for more advanced users who want to customize their analyses or run them in batch mode.

Hedge 1.8.2 is freely available for download from http://beast.community/. It is compatible with Windows, Mac OS X, and Linux operating systems. Users are advised to join the Hedge mailing list to receive updates and support from the developers and the community. Hedge 1.8.2 is a powerful tool for Bayesian phylogenetic analysis that can help researchers gain new insights into the evolution of molecular sequences.

In this article, we will provide a brief tutorial on how to use Hedge 1.8.2 for a simple phylogenetic analysis. We will use an example data set of mitochondrial DNA sequences from 10 primate species, which can be downloaded from http://beast.community/data/primate-mtDNA.nex. The data set is in NEXUS format, which is a common format for phylogenetic data.

Step 1: Launch Hedge 1.8.2

After downloading and installing Hedge 1.8.2, you can launch it by double-clicking on the icon or by using the command line. You will see the main window of Hedge, which consists of a menu bar, a toolbar, and a workspace. The workspace is where you can create and edit your analysis settings.

Step 2: Load the data set

To load the data set, go to File > Import Data > NEXUS... and select the primate-mtDNA.nex file. You will see a dialog box that shows the details of the data set, such as the number of taxa, sequences, sites, and partitions. You can also change the name and description of the data set if you wish. Click OK to import the data set into Hedge.

Step 3: Set up the analysis

After importing the data set, you will see a new tab in the workspace with the name of the data set. This tab contains four panels: Data Partitions, Site Models, Clock Models, and Trees. These panels allow you to specify various aspects of your analysis, such as how to partition your data, how to model the evolution of sites, how to model the rate variation among branches, and how to specify the tree prior.

For this tutorial, we will use the default settings for most of these panels, except for the Clock Models panel. By default, Hedge assumes a strict clock model, which means that all branches have the same rate of evolution. However, this assumption may not be realistic for many data sets, especially for mitochondrial DNA sequences that may have different rates among lineages. Therefore, we will use a relaxed clock model instead.

To change the clock model, go to the Clock Models panel and click on the drop-down menu next to Clock Model. You will see a list of available clock models in Hedge 1.8.2, such as Strict Clock, Uncorrelated Lognormal Relaxed Clock (UCLN), Uncorrelated Exponential Relaxed Clock (UCED), Random Local Clock (RLC), and Autocorrelated Relaxed Clock (AR). For this tutorial, we will choose UCLN as our clock model.

The UCLN model assumes that each branch has its own rate drawn from a lognormal distribution with a mean equal to the rate of its parent branch and a variance equal to a parameter called ucldStdev. This parameter controls how much variation there is among branch rates. A higher value means more variation and vice versa.

To specify a prior distribution for this parameter, click on the button next to ucldStdev in the Clock Models panel. You will see a dialog box that shows various options for prior distributions in Hedge 1.8.2, such as Uniform, Exponential, Lognormal, Gamma, Beta, etc. For this tutorial, we will use an Exponential prior with a mean of 0.33. This means that we expect most branch rates to be close to 0.33 substitutions per site per million years (s/s/Ma), but some may be higher or lower.

To set up this prior distribution, select Exponential from the drop-down menu next to Prior Type and enter 0.33 in the box next to Mean (or alternatively enter 3 in the box next to Rate). Click OK to apply this prior distribution to ucldStdev.

Step 4: Run the analysis

After setting up your analysis settings, you are ready to run your analysis using MCMC. To do this, go to File > Generate BEAST File... and save your analysis settings as an XML file with a name of your 061ffe29dd