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tgvaughan committed Jun 9, 2023
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Expand Up @@ -83,7 +83,7 @@ Once the sequences are added, we need to specify the sampling dates.

Open the "Tip Dates" panel and then select the "Use tip dates" checkbox.

The sampling times are encoded in the sequence names. We can tell BEAUti to use these by clicking the _Auto-configure_ button. The sampling times appear following the third vertical bar "|" in the sequence name. To extract these times, select "split on character", enter "|" (without the quotes) in the text box immediately to the right, and then select "3" from the drop-down box to the right, as shown in the figure below.
The sampling times are encoded in the sequence names. We can tell BEAUti to use these by clicking the _Auto-configure_ button. The sampling times appear following the third vertical bar "\|" in the sequence name. To extract these times, select "split on character", enter "\|" (without the quotes) in the text box immediately to the right, and then select "3" from the drop-down box to the right, as shown in the figure below.

<figure>
<a id="fig:example1"></a>
Expand Down Expand Up @@ -125,8 +125,8 @@ We first have to choose the tree prior, which in this case is MASCOT. We do this
By default, the rate dynamics for this setting is `Constant`, which means that effective population sizes and migration rates are assumed to be constant through time.
We next have to define the sampling location of the individual tips.

Initially the column **Location** should be NOT_SET for every sequence.
After clicking the _Guess_ button, you can split the sequence on the vertical bar "|" again by selecting "split on character" and entering "|" in the box. However, the locations are in the fourth group, so this time choose "4" from the drop-down menu.
Initially the column **Location** should be NOT\_SET for every sequence.
After clicking the _Guess_ button, you can split the sequence on the vertical bar "\|" again by selecting "split on character" and entering "\|" in the box. However, the locations are in the fourth group, so this time choose "4" from the drop-down menu.
After clicking the _OK_ button, the window should look like the one shown in the figure below:

<figure>
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