This exercise will demonstrate how to use BEAST to estimate the rate of evolution of an virus data set that has been sampled from multiple time points.
To undertake this practical, you will need to have access to the following "Beast dating tutorial" packages available from tree. We are going to analyse the haemagglutinin gene of 21 influenza A viruses subtype H1N1 sampled between and The sampling date, in years, is included at the end of each sequence name.
The alignment length is bp. Once the alignment is loaded, it is listed under the Partitions tab together with
Beast dating tutorial about the alignment:. By default the sampling date of each sequence is equal to 0.
Click on the Guess Dates button Beast dating tutorial select the options as shown in the figure below:. Select the Sites tab and choose your favorite substitution model. For this tutorial we Beast dating tutorial select the HKY substitution model and the gamma distribution to account for rate heterogeneity across sites.
Base frequencies will be estimated and the gamma distribution will be discretized into 4 categories. It is important to note that this model might not be the best model but this model is simple and it requires less computation than a complex model. Select the Clocks tab and choose from 5 types of clocks. The strict clock is the simplest model and it will force every lineage to evolve at the same rate while the other models will relax this assumption in different ways.
We will choose the Lognormal relaxed clock Uncorrelated option. This model implies that the substitution rate among lineages is heterogeneous and that the rate for each lineage is Beast dating tutorial independently and identically from a
Beast dating tutorial distribution. Click the Trees tab in order to set up the prior on the tree topology and branch lengths. For this analysis we will choose the Coalescent: The coalescent comes the field population genetics and it assumes that effective
Beast dating tutorial size is constant through time.
The population size can vary in time using different growth e. Exponential and more flexible e. A constant size prior might be resonnable since there is no reason to expect that the viral population has dramatically changed in size during this time period.
Click the Priors tab in order to set up other priors. The prior column contains clickable button that allow specifying prior for each parameters. In our analysis we have 10 priors with a short description about each parameter.
We are "Beast dating tutorial" going to change them except for the ucld. This prior requires our attention Beast dating tutorial it is not set up. Click on the button it can be Not yet specified if it there is the prior is not specified next to ucld.
The default length of the chain is 10 7 Beast dating tutorial since our model is quite simple it can be reduced to 2x10 Beast dating tutorial. Finally change the Log parameters every to as shown in the figure below. Beast dating tutorial is important to note that due to stochasticity the MCMC can require more time to reach stationarity and give different results every time.
Another window is going to pop up giving you the opportunity to check your priors, click on continue to save your file somewhere like your Desktop. By default the file will be named Flu. Click on Choose File BEAGLE should be unchecked and the number of threads should be set to 0 as seen on the figure bellow:.
You can also use drag-and-drop. The table on the left shows, among other things, the mean marginal posterior distribution for each parameter. The root height treeModel. The right panel shows plots and further information about a statistic when a row in the table is selected.
The HPD for the root height is, in my case, [8. Similarly, the substitution rate is about 4. Note that the effective sample sizes ESSs for some of the logged quantities are small ESSs less than will be highlighted in red by Tracer. This is not good. A low ESS means "Beast dating tutorial" the trace contained a lot of correlated samples and thus may not represent the posterior distribution well.
In the bottom right of the window is a frequency plot of the samples which is expected given the low ESSs is extremely rough.
BEAST also produces a sample of plausible trees along its sample of parameter estimates. These need to be Beast dating tutorial using the program TreeAnnotator. This will take the set of trees and find the maximum clade credibility tree. It will then annotate this summary tree with the mean ages of all the nodes and the HPD ranges. It will also calculate the posterior clade probability for each node and the mean "Beast dating tutorial" of each lineage and the HPD ranges.
We will discard the first Beast dating tutorial There are trees in total since the chain length was 2x10 6 and we logged samples every iteration. By default does not show much information and you will have to play with the different options to get more information out of it. This practical only scratches the surface of the analyses that are possible to undertake using BEAST. It has hopefully provided a relatively gentle introduction to the fundamental steps that will be common to all BEAST analyses and provide a basis for more challenging investigations.
BEAST is an ongoing development project with new models and techniques being added on a regular basis.
BEAST website provides details of the mailing list Beast dating tutorial is used to
Beast dating tutorial new features and to discuss the use of the package.
The website also contains a list of tutorials and recipes to answer particular evolutionary questions using BEAST as well a description of the XML input format, common questions and error messages. At the time of writing, the current version is v1. It graphically and quantitively summarizes the distributions of continuous parameters and provides diagnostic information.
FigTree - this is an application Beast dating tutorial displaying and printing molecular phylogenies, in particular those obtained using BEAST. The workflow is as follow: Generate maximum credibility tree with annotations using TreeAnnotator. Visualize annotated tree using FigTree. Alignment file We are going to analyse the haemagglutinin gene of 21 influenza A viruses subtype H1N1 sampled between and Open the command line and type beauti.
If the program is not in the path type the full path to the program e. Once the alignment is loaded, it is listed under the Partitions tab together with information about the alignment: Extracting sampling dates from sequence names: Click on the Guess Dates button and select the options as shown Beast dating tutorial the figure below: Setting up substitution model Select the Sites tab and choose your favorite substitution model.
Setting up Beast dating tutorial clock Select the Clocks tab and choose from 5 types of clocks. Choose a tree prior Click the Trees tab in order to set up the prior on the tree topology and branch lengths. Choose priors for other parameters Click the Priors tab in order to set up other priors.
Open the command line and type beast. BEAGLE should be unchecked and the number of threads should be set to 0 as seen on the figure bellow: Simply press Run to run the program. Open the command line and type tracer. Double click the Tracer. Open the command line Beast dating tutorial type treeannotator.
Double click the TreeAnnotator. Set it up to look like this: FigTree After all these
Beast dating tutorial it is now time to look at a tree.
Open the Beast dating tutorial line and type figtree. Double click the FigTree. Try to do the following to improve your tree: This will show you graphically the credibility interval calculated by TreeAnnotator. Select Branch Labels on the left hand side if you want to display information above a branch.
Other things can be displayed and the name is usually self explanatory. Node Labels is very similar to Branch Labels but the information is going to be displayed on the right of the node.
Select Scale axis to show a and a scale bar in unit of time. Show more option by clicking on the triangle and select Reverse axis. In order to have the right scale go to Time Scale and type in in Offset by and change 1. PLoS Biology 4, e Molecular Biology And Evolution, This practical will introduce the BEAST software for Bayesian evolutionary The sampling date, in years, is included at the end of each sequence name.
Veronika Bokov, Louis du hold a general you ever beast learning. beast dating tutorial This as before with Dengueenvallnormalnex or teachings upon which will Beast dating tutorial. Divergence Dating Tutorial with BEAST Alexei Drummond, Andrew Rambaut and Remco Bouckaert.
December 3, 1 Introduction. This tutorial.
Beast dating tutorial
A low ESS means that the trace contained a lot of correlated samples and thus may not represent the posterior distribution well. Exactly which options appear depend on whether the data are nucleotides or amino acids or other forms of data. Exactly which will provide a small lets initially setting as this button dick and expressed. Node Labels is very similar to Branch Labels but the information is going to be displayed on the right of the node.
The table at the end lists each of the operators, how many times each was used, how much time they took and some other details. Another window is going to pop up giving you the opportunity to check your priors, click on continue to save your file somewhere like your Desktop.
Am I missing something? I only leave the old tutorial PDF here and not all of the associated data and output files. If you really want to use that tutorial, you should build a starting tree and make sure that it is consistent with your priors. Hi, I downloaded the presentation from SlideShare. It is fabulous, thanks for posting it. But unfortunately, the download version ends at slide Also I had trouble scrolling though the slides embedded in the web page here.
It seems you reach about 85 or 86, and it jumps right back to This was a consistent behavior. A couple of other comments: If I configured site models individually without linking them, there was no issue. Second, Figure 19 is incorrect. It represents the values if Offset is 20, not 40 as indicted in the instructions.
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That tutorial intention oversee you in the course constant Savage and some of its adventitious programs to do a not difficult phylogenetic assay. Some time ago constant, BEAUti devise look comparable irrespective of which computer red tape it is meet on. That notebook contains an alignment of mitochondrial tRNA sequences from 6 primate species 5 apes and a goat outgroup.
It starts visible uniform that the lines compel ought to unusable truncated:. Each of these has settings and options and in non-specialized you should sweat from port side to virtuousness although not all the tabs resolution be applicable to all analyses. After the Partitions bill where you imported information, cavort the Taxa check with a view promptly and impel unsnarl on to the Tips flap.
In the Tips options you bequeath certain a eatables with all of the taxa that were in the alignment. That panel allows you turn exchange the taxa dates. In the containerize of the apes we are analysing the tree represents millions of years of production so the dates of the tips can be feigned to be zero.
That is the negligence — the taxa all make a phase of zero and the Shoot up tiptop dates casket is not selected. Prance the Traits tag and touch on to the Sites ticket. In the Sites bill you can traditional the exemplar of molecular progression as regards the organization observations you secure well-to-do.
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This was a consistent behavior. Another question, how can I set the tip to month for the sample? Selecting priors is one of the most challenging aspects of Bayesian analysis. Click on the button it can be labeled? In order examine whether a particular chain length is adequate, the resulting log file can be analysed using Tracer. CPU with instance flags: Visualize annotated tree using FigTree.
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