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Tiny changes to layout.

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tgvaughan committed Nov 5, 2018
1 parent ed00394 commit 130a54992d9f506266f69b40184bb3040cf7e8e3
Showing with 5 additions and 2 deletions.
  1. +5 −2 README.md
@@ -210,7 +210,9 @@ After the program has run, find the h1n1_ucld.tre and open it in [icytree](icytr
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Optional exercise 1: Use the BEAUTI window, which we left open, to sample from the prior distribution. This is useful to assess whether the data are informative about parameters of interest. To do this, go to the MCMC tab and tick the SampleFromPrior box. Change the names of the output log and trees files to h1n1_ucld_prior.log and h1n1_ucld_prior.trees and go to File, Save as, and save it as h1n1_UCLD_prior.xml. This analysis will run much faster because it does not need to calculate the phylogenetic likelihood. After it has run, load the log file with that from the posterior.
## Optional exercise 1
Use the BEAUTI window, which we left open, to sample from the prior distribution. This is useful to assess whether the data are informative about parameters of interest. To do this, go to the MCMC tab and tick the SampleFromPrior box. Change the names of the output log and trees files to h1n1_ucld_prior.log and h1n1_ucld_prior.trees and go to File, Save as, and save it as h1n1_UCLD_prior.xml. This analysis will run much faster because it does not need to calculate the phylogenetic likelihood. After it has run, load the log file with that from the posterior.

> **Question**: Does it seem like our data are driving our estimates of evolutionary rates and timescales (hint: compare the prior and the posterior for the tree height, as in [Figure 18](#f18:f18), and for the rate.mean parameters).
<figure>
@@ -220,7 +222,8 @@ Optional exercise 1: Use the BEAUTI window, which we left open, to sample from t
</figure>


Optional exercise 2: Use the BEAUTI window, which we left open, to set up a strict clock. To do this go to the Clock Model tab and select Strict Clock. In the MCMC tab change the output file names to h1n1_sc.log, h1n1_sc.trees. Save it as h1n1_sc.xml and run it in BEAST. Compare the rate and node age estimates to those from the relaxed clock used here.
## Optional exercise 2
Use the BEAUTI window, which we left open, to set up a strict clock. To do this go to the Clock Model tab and select Strict Clock. In the MCMC tab change the output file names to h1n1_sc.log, h1n1_sc.trees. Save it as h1n1_sc.xml and run it in BEAST. Compare the rate and node age estimates to those from the relaxed clock used here.


# Relevant References

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