Skip to content
Permalink
Browse files

add tree annotator screenshot

  • Loading branch information...
rbouckaert committed Mar 24, 2019
1 parent 106f2de commit 4237ab1c184e0bc72e07c094ba2bc28dca1e7cdb
@@ -355,23 +355,34 @@ overlaid:

## Summarising the trees

Use the program TreeAnnotator to summarise the tree and view the results
in Figtree (Figure \[fig:RSV2tree\]).
Use the program TreeAnnotator to summarise the tree. TreeAnnotator is an application that
comes with BEAST.

<figure>
<a name="fig:RSV2tree"></a>
<img style="width:80.0%;" src="figures/RSV2_mcc_tree.png" alt="">
<figcaption>Figure 14: The Maximum clade credibility tree for the G gene of 129 RSVA-2 viral samples.</figcaption>
<figcaption>Figure 14: TreeAnnotator for creating a summary tree from a posterior tree set.</figcaption>
</figure>
<br>

DensiTree with clade height bars for clades with over 50% support. Root

Summary trees can be viewed using FigTree (a program separate from BEAST) and
DensiTree (distributed with BEAST).

<figure>
<a name="fig:RSV2tree"></a>
<img style="width:80.0%;" src="figures/RSV2_mcc_tree.png" alt="">
<figcaption>Figure 15: The Maximum clade credibility tree for the G gene of 129 RSVA-2 viral samples.</figcaption>
</figure>
<br>

Below a DensiTree with clade height bars for clades with over 50% support. Root
canal tree represents maximum clade credibility tree.

<figure>
<a name="fig:RSV2tree"></a>
<img style="width:80.0%;" src="figures/DensiTree.png" alt="">
<figcaption>Figure 15: The posterior tree set visualised in DensiTree.</figcaption>
<figcaption>Figure 16: The posterior tree set visualised in DensiTree.</figcaption>
</figure>
<br>

@@ -393,7 +404,7 @@ which is a prior that ensures dependence between population sizes.
<figure>
<a name="fig:BEAUti\_priors2"></a>
<img style="width:80.0%;" src="figures/BEAUti_priors2.png" alt="">
<figcaption>Figure 16: Priors</figcaption>
<figcaption>Figure 17: Priors</figcaption>
</figure>
<br>

@@ -410,7 +421,7 @@ number of changes, so it could be used as an alternative tree prior.
<figure>
<a name="fig:BEAUti\_init"></a>
<img style="width:80.0%;" src="figures/BEAUti_init.png" alt="">
<figcaption>Figure 17: Initialization panel</figcaption>
<figcaption>Figure 18: Initialization panel</figcaption>
</figure>
<br>

@@ -426,7 +437,7 @@ the menu Analysis/Bayesian Skyline Reconstruction.
<figure>
<a name="fig:tracerBSP1"></a>
<img style="width:80.0%;" src="figures/tracerBSP1.png" alt="">
<figcaption>Figure 18: Bayesian Skyline Reconstruction in Tracer</figcaption>
<figcaption>Figure 19: Bayesian Skyline Reconstruction in Tracer</figcaption>
</figure>
<br>

@@ -437,7 +448,7 @@ entry for age of youngest tip to 2002.
<figure>
<a name="fig:tracerBSP2"></a>
<img style="width:80.0%;" src="figures/tracerBSP2.png" alt="">
<figcaption>Figure 19: Bayesian Skyline Reconstruction dialog in Tracer</figcaption>
<figcaption>Figure 20: Bayesian Skyline Reconstruction dialog in Tracer</figcaption>
</figure>
<br>

@@ -448,7 +459,7 @@ the median and 95% HPD intervals are plotted. After selecting the
<figure>
<a name="fig:tracerBSP3"></a>
<img style="width:80.0%;" src="figures/tracerBSP3.png" alt="">
<figcaption>Figure 20: Bayesian Skyline Reconstruction</figcaption>
<figcaption>Figure 21: Bayesian Skyline Reconstruction</figcaption>
</figure>
<br>

BIN -39.9 KB (20%) figures/RSV2_mcc_tree.pdf
Binary file not shown.
BIN +33.2 KB (200%) figures/RSV2_mcc_tree.png
Binary file not shown.
Binary file not shown.

Large diffs are not rendered by default.

Oops, something went wrong.

0 comments on commit 4237ab1

Please sign in to comment.
You can’t perform that action at this time.