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refined latex to md conversion

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Müller  Nicola
Müller Nicola committed Jun 21, 2018
1 parent 4710cff commit 0dac8eede4f7fd4c170464d1ca63e8027632da1f
Showing with 10 additions and 10 deletions.
  1. +10 −10 README.md
@@ -134,7 +134,7 @@ evolutionary tree for a given locus). The data for each locus is stored as one
alignment in its own NEXUS file. Taxa names in each alignment have to be unique,
but duplicates across alignments are fine.

To load a NEXUS format alignment, click the button with the plus symbol ($+$) in
To load a NEXUS format alignment, click the button with the plus symbol (+) in
the lower left corner of the main **Partitions** tab. For this tutorial,
navigate to the **examples/nexus** subfolder inside the **beast**
application folder, and select all of the first seven NEXUS files. They should
@@ -197,7 +197,7 @@ Ploidy should be based on the mode of inheritance for each gene. By convention,
nuclear genes in diploids are given a ploidy of 2.0. Because mitochondrial and Y
chromosome genes are haploid even in otherwise diploid organisms, and also
inherited only through the mother or the father respectively, their effective
population size $N_e$ is only one quarter that of nuclear genes. Therefore if
population size N<sup>e</sup> is only one quarter that of nuclear genes. Therefore if
nuclear gene ploidy is set to 2.0, mitochondrial or Y chromosome gene ploidy
should be set to 0.5. In this analysis all genes are from nuclear loci and their
ploidy should be left at the default value of 2.0.
@@ -284,7 +284,7 @@ differences in substitution rates, so we should constrain the per-species branch
rates to a reasonable range of values. Click the button next to
_branchRates.Species_ to define this range. Change _Lower_ to 0.1 and
_Upper_ to 10.0, which means that the fastest branch rate can not be more than
$100\times$ that of the slowest branch rate.
100 times that of the slowest branch rate.


<figure>
@@ -324,8 +324,8 @@ be set relative to the total length of the chain. Sampling too often will result
in very large files with little extra benefit in terms of the precision of the
analysis. Sample too infrequently and the log file will not contain much
information about the distributions of the parameters. You probably want to aim
to store no more than $10000$ samples so this should be set to no less than
$\text{chain length}\div10000$. For this exercise, leave the default **Store
to store no more than 10000 samples so this should be set to no less than
(chain length)/10000. For this exercise, leave the default **Store
Every** and **Log Every** settings in place.

If you are using Windows then we suggest you add the suffix _.txt_ to the
@@ -387,11 +387,11 @@ confidence interval. The HPD for the sum of rate changes suggests that either 0,
For any Bayesian analysis, it is very important to compare your findings with
the prior distribution. The default prior distribution for the number of
substitution rate shifts for a random local clock is a Poisson distribution
with the $\lambda$ parameter fixed at $\ln(2) \approx 0.69$. The prior
with the \lambda parameter fixed at ln(2), which is approximately 0.69. The prior
probability of zero rate changes for the default distribution is equal to
50\%. Tracer reported that around 1250 samples had zero rate shifts,
out of $9000000 \div 5000 = 1800$ post-burnin posterior samples. This means that after
adding data, our belief in a strict clock increased from 50\% to about 70\%,
50%. Tracer reported that around 1250 samples had zero rate shifts
(out of 9000000/5000 = 1800) post-burnin posterior samples. This means that after
adding data, our belief in a strict clock increased from 50% to about 70%,
a very modest change. The data in this tutorial suggests that a strict clock
applies to pocket gophers, but falls far short of any standard of proof.

@@ -401,7 +401,7 @@ BEAST also produces a sample of plausible trees. These can be summarized using
the program **TreeAnnotator**. This will take the set of trees and identify
a single tree that best represents the posterior distribution. It will then
annotate this selected tree topology with the mean ages of all the nodes as well
as the 95\% HPD interval of divergence times for each clade in the selected
as the 95% HPD interval of divergence times for each clade in the selected
tree. It will also calculate the posterior clade probability for each node. Run
the **TreeAnnotator** program and set it up to look like in the figure below.

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