author	level	title	subtitle	beastversion
Author I. Name	Intermediate	Tutorial template	Template for an empty tutorial	2.4.2

Background

This is a template tutorial and style guide to help formatting Markdown tutorials.

Please start the tutorial by adding some background about the tutorial in this section, clearly explaining the question/problem and the type of analysis that the methods in the tutorial should be used for. In the next section please add a short description of all the programs or packages used in the tutorial. The tutorial exercise should follow this part. Please add a short explanation on the dataset used in the tutorial before starting with the exercise. Please also add a section after the exercise interpreting the results. End your tutorial with some useful links.

Some of the text in this tutorial template is just dummy filler text. Please do not try to understand it.

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Programs used in this Exercise

BEAST2 - Bayesian Evolutionary Analysis Sampling Trees 2

BEAST2 is a free software package for Bayesian evolutionary analysis of molecular sequences using MCMC and strictly oriented toward inference using rooted, time-measured phylogenetic trees {% cite Bouckaert2014 --file Tutorial-Template/master-refs.bib %}. This tutorial uses the BEAST2 version 2.4.2.

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Practical: Exercise title

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This is a subsection

Quisque a dictum erat. Curabitur congue sapien sit amet pharetra pretium. Proin posuere euismod velit, eget faucibus ex varius id. Fusce sodales maximus malesuada. Mauris auctor dui in justo interdum egestas. Cras dapibus commodo nulla vitae congue. Vestibulum sit amet justo sit amet ex pretium bibendum. Donec ac mollis lorem, vel semper enim. Suspendisse sit amet auctor dui. Nullam ac efficitur mauris. Proin aliquam tincidunt felis nec semper. Vestibulum vestibulum, eros sit amet consectetur blandit, elit dolor posuere sem, a porta purus odio sit amet quam. Quisque dapibus erat sem, at vulputate libero dapibus sit amet. Mauris rhoncus odio nisl, nec interdum lacus consequat nec. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos.

Etiam tincidunt porttitor rutrum. Nulla facilisi. Mauris vehicula, justo ac ultricies tempus, quam erat hendrerit dui, vel pharetra sapien nibh vel ex. Sed molestie eu dui in laoreet. Pellentesque ultrices, orci vitae lacinia suscipit, erat sapien elementum ligula, sit amet viverra ante lorem eget elit. Cras euismod felis libero, pharetra lobortis arcu congue vehicula. Nullam posuere dapibus mauris, eget vulputate ligula auctor eget. Aenean et tempus est. Aliquam vehicula arcu vitae metus dictum viverra. Aliquam vitae purus mauris. Nullam interdum mauris eget sagittis consequat. Quisque in orci elementum, eleifend tortor eget, bibendum orci. Etiam aliquet dolor non neque semper fermentum. Praesent vitae venenatis mi, ut faucibus ligula. Phasellus vitae lorem neque. Interdum et malesuada fames ac ante ipsum primis in faucibus.

This is a sub-subsection

Etiam posuere urna ut condimentum sagittis. Suspendisse posuere, ex nec eleifend fringilla, nisl augue posuere augue, elementum mollis justo felis sed purus. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Mauris efficitur eros ut turpis elementum vestibulum. Sed sit amet nisi at nunc luctus laoreet id ac enim. Aliquam elementum risus id urna dictum fringilla. Aenean lobortis, risus euismod molestie pulvinar, massa odio pharetra nulla, vitae facilisis neque magna sed lorem. Praesent ipsum enim, commodo ut pharetra in, sollicitudin ac massa. Donec et interdum mauris. Ut molestie, risus quis fermentum placerat, diam risus posuere nisi, eget viverra tortor neque ac sem. Donec viverra magna non dolor aliquam, in suscipit massa facilisis. Suspendisse congue arcu sed risus consectetur commodo. Aenean metus odio, volutpat at tincidunt id, ullamcorper in dui. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Cras ut sem in odio sodales iaculis non quis neque.

Quisque non mollis massa, nec eleifend dolor. Proin porta elit metus, a lobortis enim venenatis ac. Nam scelerisque consectetur mi et gravida. Vestibulum placerat, est vitae euismod finibus, purus nisl viverra quam, eget condimentum mauris magna vel nisl. Phasellus pretium vitae diam in volutpat. Cras gravida non quam ut consectetur. Vivamus congue vulputate lorem.

This is another subsection

Praesent sodales est in tempor commodo. Suspendisse nulla metus, gravida eget malesuada vel, viverra eu felis. In vitae leo facilisis, ornare nunc nec, tempor tortor. Duis pretium mi eros, at consequat neque tincidunt eget. Mauris vestibulum venenatis arcu, eget lacinia arcu faucibus ut. Phasellus aliquam dui ipsum, a eleifend lacus fermentum at. Suspendisse congue orci quis ante consequat ornare. Integer a massa blandit, vestibulum eros ut, pulvinar augue. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos.

Quisque a urna a massa congue rhoncus. Donec bibendum tempus velit. Nam varius augue sit amet lacinia hendrerit. Proin tincidunt massa ut mi vestibulum placerat. Phasellus eget dui molestie, aliquet libero efficitur, vehicula ex. Pellentesque ultricies ante leo, eu lobortis odio convallis id. Donec vitae risus dui. Nulla orci velit, ultricies sed finibus quis, blandit quis arcu. Morbi non neque non odio rutrum condimentum. Vivamus libero metus, vehicula vitae elit ac, tincidunt pretium dui. Proin condimentum fringilla diam, blandit blandit nisl dapibus vel. Proin ante felis, accumsan eget ligula et, lobortis dictum nunc. Mauris a ante dignissim ipsum tincidunt tristique.

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Tutorial style guide

Text styling

This is how to write italic text.

This is how to write bold text.

This is how to write bold and italic text.

Do text superscripts like this 7^th, x^2y or x^(2y + 3z).

Lists

Unnumbered lists

• Lorem ipsum dolor sit amet, consectetur adipiscing elit.
• Integer pharetra arcu ut nisl mollis ultricies.
  • Fusce nec tortor at enim cursus dictum.
  • Phasellus nec urna quis velit eleifend convallis sodales nec augue.
• In iaculis turpis in massa facilisis, quis ultricies nibh ultricies.
• Nam vitae turpis eu lacus imperdiet mollis id at augue.
• Sed sed turpis ac dolor mollis accumsan.

Numbered lists

1. Lorem ipsum dolor sit amet, consectetur adipiscing elit.
2. Integer pharetra arcu ut nisl mollis ultricies.
   1. Fusce nec tortor at enim cursus dictum.
   2. Phasellus nec urna quis velit eleifend convallis sodales nec augue.
3. In iaculis turpis in massa facilisis, quis ultricies nibh ultricies.
4. Nam vitae turpis eu lacus imperdiet mollis id at augue.
5. Sed sed turpis ac dolor mollis accumsan.

Mixed lists

1. Lorem ipsum dolor sit amet, consectetur adipiscing elit.
2. Integer pharetra arcu ut nisl mollis ultricies.
   • Fusce nec tortor at enim cursus dictum.
   • Phasellus nec urna quis velit eleifend convallis sodales nec augue.
3. In iaculis turpis in massa facilisis, quis ultricies nibh ultricies.
4. Nam vitae turpis eu lacus imperdiet mollis id at augue.
5. Sed sed turpis ac dolor mollis accumsan.

Figures

Figure 1: This figure is 25% of the page width.

Figure 2: This figure is only 10% of the page width.

Code

A bit of inline monospaced font can be made like this. Larger code blocks can be made by using the code environment:

Java:

public class HelloWorld {

    public static void main(String[] args) {
        // Prints "Hello, World" to the terminal window.
        System.out.println("Hello, World");
    }

}

XML:

	<BirthDeathSkylineModel spec="BirthDeathSkylineModel" id="birthDeath" tree="@tree" contemp="true">
	      <parameter name="origin" id="origin" value ="100" lower="0."/>    
	      <parameter name="R0" id="R0" value="2" lower="0." dimension ="10"/>
	      <parameter name="becomeUninfectiousRate" id="becomeUninfectiousRate" value="1" lower="0." dimension ="10"/>
	      <parameter name="samplingProportion" id="samplingProportion" value="0."/>
	      <parameter name="rho" id="rho" value="1e-6" lower="0." upper="1."/>
	</BirthDeathSkylineModel>

R:

	> myString <- "Hello, World!"
	> print (myString)
	[1] "Hello, World!"

Equations

Inline equations: {% eqinline \dot{x} = \sigma(y-x) %}

Displayed equations: {% eq \left( \sum_{k=1}^n a_k b_k \right)^2 \leq \left( \sum_{k=1}^n a_k^2 \right) \left( \sum_{k=1}^n b_k^2 \right) %}

Instruction boxes

Use block-quotes for step-by-step instruction that the user should perform (this will produce a framed box on the website):

The data we have is not the data we want, and the data we need is not the data we have.

We can input any formatted text in here:

• Even
• Lists

or equations:

{% eq (x_1, \ldots, x_n) \left( \begin{array}{ccc} \phi(e_1, e_1) & \cdots & \phi(e_1, e_n) \ \vdots & \ddots & \vdots \ \phi(e_n, e_1) & \cdots & \phi(e_n, e_n) \end{array} \right) \left( \begin{array}{c} y_1 \ \vdots \ y_n \end{array} \right) %}

Hyperlinks

Add links to figures like this:

• Figure 1 is 25% of the page width.
• Figure 2 is 10% of the page width.

Add links to external URLs like this.

Links to equations or different sections within the same document are a little buggy.

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Useful Links

• Bayesian Evolutionary Analysis with BEAST 2 {% cite BEAST2book2014 --file Tutorial-Template/master-refs.bib %}
• BEAST 2 website and documentation: http://www.beast2.org/
• BEAST 1 website and documentation: http://beast.bio.ed.ac.uk
• Join the BEAST user discussion: http://groups.google.com/group/beast-users

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Relevant References

{% bibliography --cited --file Tutorial-Template/master-refs.bib %}