Setting up age distribution from BEAST MCC tree

[evandiego83]

Hi,

Thank you for the wonderful software. I am trying to plot the age distributions and tried to follow your tutorial but I am stumped as I don't get any age distributions. My file is a nexus file from treeannotator and looks like this:

(((((68[&length_range={0.5715086893601,7.557567357345},height_95%_HPD={4.495890410957597,4.495890410960293},rate_95%_HPD={0.005018198849218783,0.02724086442802083},length_95%_HPD={1.2248.......

I want to see the height_95%_HPD as the age distribution on the tree can you please send me further instructions?

Thanks you
Evan

[arklumpus]

Hi, I'm glad you're finding TreeViewer useful!

The file produced by TreeAnnotator indeed does not contain the full age distributions (i.e., the things that can be plotted as a violin plot), but it does contain the 95% HPDs, which can be plotted as node bars.

You have a few options:

• Plot the HPDs as node bars

  To do this, after opening the TreeAnnotator output file, you need to open the list of plot elements (Modules tab > Plot actions) and add a new instance of the Node bars module. You can then expand the options for this module to make sure that the correct attribute has been selected and you can play with the appearance options to change the look of the bars.

• Use TreeViewer to compute the consensus tree and create age distribution violin plots

  If you wish to plot the distributions as violin plots, you don't need to use TreeAnnotator. You can directly open the .trees file produced by BEAST, and TreeViewer will automatically compute the consensus tree. You can then follow the rest of the age distribution tutorial.

• Add the age distribution violin plots to the TreeAnnotator tree

  If you don't want to use the consensus tree computed by TreeViewer, you can open the TreeAnnotator file and then add the .trees file as an attachment to the plot. Then, you should enable the Set up age distributions (attachment) module and select the correct attachment. If you then enable the Age distributions Plot action module, the age distributions from the .trees file will be shown on the tree. This is similar to the tutorial on plotting multiple age distributions.

Note that when computing the age distributions, TreeViewer also computes the HPDs (which you could still plot, in addition to the violin plots).