Skip to content

Commit

Permalink
correct merger artifacts
Browse files Browse the repository at this point in the history
  • Loading branch information
Müller Nicola committed Jun 14, 2018
1 parent 474026d commit 3a42c3b
Showing 1 changed file with 0 additions and 7 deletions.
7 changes: 0 additions & 7 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -230,21 +230,14 @@ To get the actual inferred probabilities of each node being in any of the 3 loca
We can now open the MCC tree using FigTree. To do this, run FigTree and choose _File >> Open_. Using the dialog box, select the file "mcc.trees" generated by TreeAnnotator.

Each node in the displayed tree has several traits. Among them are those called Hong_Kong, New_York and New_Zealand. The value of those traits is the probability of that node being in that location as inferred using MASCOT. To view these probability values, select the "Node Labels" checkbox and click the arrow immediately to the left of this pox to expand it. Selecting Hong_Kong, New_York and New_Zealand from the "Display" drop-down menu will cause the probabilities of the internal nodes being in each of these states to be displayed on the tree, as shown in the figures below.
>>>>>>> ec5ebe3cd74dfaa3d187d8f57a4a96a956fcd712

<figure>
<a id="fig:example1"></a>
<img style="width:100%;" src="figures/ColorsTree.png" alt="">
<figcaption>Figure 13: Inferred node locations.</figcaption>
</figure>

<<<<<<< HEAD
It should be mentioned here that the inference of nodes being in a particular location make some simplifying assumptions. Amongst other, we assume that there are no other locations where lineages could have been.

=======
We can now determine if lineages ancestral to samples from New York are actually inferred to be from Hong Kong, or the probability of the root being in any of the locations. It should here be mentioned that the inference of nodes being in a particular location makes some simplifying assumptions, such as that there are no other locations (i.e. apart from the sampled locations) where lineages could have been.
>>>>>>> ec5ebe3cd74dfaa3d187d8f57a4a96a956fcd712

----

Expand Down

0 comments on commit 3a42c3b

Please sign in to comment.