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Densitree paragraph

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KonstantinHoffmann committed Jul 29, 2019
1 parent ec27569 commit 04c6a4a164e03bd24886625f33191e334ed9207e
Showing with 2 additions and 556 deletions.
  1. +2 −3 README.md
  2. +0 −553 precooked_runs/cpacific_burnin_removed.trees
@@ -289,10 +289,9 @@ Interestingly most of the diversification events happened in the past 1500 years

### Compare tree topologies with `DensiTree`

The first branching event after the root has a fairly low support in our MCC-tree. This means that the topology is just the most likely one, but not neccessarily the correct one as other might also have a decent support. To visualize these other topologies `DensiTree` is a nice tool. A detailed description on how to use `DensiTree` is in the tutorial [Introduction to BEAST2](https://taming-the-beast.org/tutorials/Introduction-to-BEAST2/). Note that we first need to create a tree log file, where the burn-in is discarded. For this purpose you can use the program `LogCombiner`, which is included in the BEAST2 installation.
The first branching event after the root has a fairly low support in our MCC-tree. This means that the topology is just the most likely one, but not neccessarily the correct one as other might also have a decent support. To visualize these other topologies `DensiTree` is a nice tool. A detailed description on how to use `DensiTree` is in the tutorial [Introduction to BEAST2](https://taming-the-beast.org/tutorials/Introduction-to-BEAST2/).

> Open LogCombiner. Set the `File Type` to `Tree Files`, press on `+` and select the tree log file (`cpacific.trees`). Click on the `Burnin (percentage)` of your file and set it (in our case) to **50**. Click on `Choose File...` on the bottom and type your output file name (e.g. **cpacific_burnin_removed.trees**). Finally press `Run` and wait until it is finished.
> Open DensiTree, click on `File > Load` and select your truncated log file (`cpacific_burnin_removed.trees`).
> Open DensiTree, click on `File > Load` and select your log file (`cpacific.trees`). Click on the `Burn in`-tab on the right panel and set the burn in (in our case) to $50$.
<figure>
<img style="width:100%;" src="figures/densitree.png" alt="">

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