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rbouckaert committed Mar 24, 2019
1 parent 8d0449b commit 106f2dea9ccac2184acd67b0c89ce046d3ab763e
Showing with 9 additions and 9 deletions.
  1. +9 −9 README.md
@@ -49,7 +49,7 @@ The following software will be used in this tutorial:
the time of writing, the current version is v`1.4.3`. It is
available for download from [http://beast.community/figtree](http://beast.community/figtree).

## The NEXUS alignment {#the-nexus-alignment .unnumbered}
## The NEXUS alignment

The data is in a file called
[RSV2.nex](https://github.com/CompEvol/beast2/blob/master/examples/nexus/RSV2.nex?raw=true).
@@ -87,7 +87,7 @@ something like this:
</figure>
<br>

## Tip dates {#tip-dates .unnumbered}
## Tip dates

By default all the taxa are assumed to have a date of zero (i.e. the
sequences are assumed to be sampled at the same time). In this case, the
@@ -122,7 +122,7 @@ The dates panel should now look something like this:
</figure>
<br>

## Setting the substitution model {#setting-the-substitution-model .unnumbered}
## Setting the substitution model

We will use the HKY model with empirical base frequencies for all three
partitions. To do this first link the site partitions and then choose
@@ -181,7 +181,7 @@ file to `400`.
</figure>
<br>

## Running BEAST {#running-beast .unnumbered}
## Running BEAST

Save the BEAST file (e.g. `RSV2.xml`) and run it in BEAST.

@@ -264,7 +264,7 @@ Total calculation time: 106.096 seconds
End likelihood: -6102.669168760964
```

## Analysing the BEAST output {#analysing-the-beast-output .unnumbered}
## Analysing the BEAST output

Note that the effective sample sizes (ESSs) for many of the logged
quantities are small (ESSs less than 100 will be highlighted in red by
@@ -353,7 +353,7 @@ overlaid:
</figure>
<br>

## Summarising the trees {#summarizing-the-trees .unnumbered}
## Summarising the trees

Use the program TreeAnnotator to summarise the tree and view the results
in Figtree (Figure \[fig:RSV2tree\]).
@@ -376,12 +376,12 @@ canal tree represents maximum clade credibility tree.
<br>


## Questions {#questions .unnumbered}
## Questions

> In what year did the common ancestor of all RSVA viruses sampled live?
> What is the 95% HPD?
## Bonus section: Bayesian Skyline plot {#bonus-section-bayesian-skyline-plot .unnumbered}
## Bonus section: Bayesian Skyline plot

We can reconstruct the population history using the Bayesian Skyline
plot. In order to do so, load the XML file into BEAUti, select the
@@ -452,7 +452,7 @@ the median and 95% HPD intervals are plotted. After selecting the
</figure>
<br>

## Questions {#questions-1 .unnumbered}
## Questions

>
>1. By what amount did the effective population size of RSVA grow from

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