Bayesian phylogenetics: clock models - Revision history

Gorm: /* Questions */

2026-04-22T13:43:44Z

Questions

← Older revision		Revision as of 15:43, 22 April 2026
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	'''Question 3'''		'''Question 3'''

	~~After the first BEAST run, inspect the output in Tracer.~~

	After the first BEAST run, inspect the output in Tracer. What indications are there that the initial run is not yet satisfactory? In your answer, mention burn-in, trace behaviour, and ESS, and include at least one relevant screendump from Tracer.		After the first BEAST run, inspect the output in Tracer. What indications are there that the initial run is not yet satisfactory? In your answer, mention burn-in, trace behaviour, and ESS, and include at least one relevant screendump from Tracer.

Gorm: /* Questions */

2026-04-22T10:50:43Z

Questions

← Older revision		Revision as of 12:50, 22 April 2026
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	'''Question 2'''		'''Question 2'''

	In the first analysis, the tutorial uses a strict molecular clock. What ~~does this~~ assumption ~~mean biologically and statistically? Why might~~ this ~~be a reasonable first~~ model ~~to try~~, and ~~what kinds of evolutionary patterns~~ would ~~violate~~ this assumption?		In the first analysis, the tutorial uses a strict molecular clock. What is the assumption behind this model? Explain what is being assumed about evolutionary rates on different branches, and why this means that expected branch length depends on branch duration and a single shared substitution rate. Also describe a pattern in the data that would suggest this assumption may be unrealistic.

	'''Question 3'''		'''Question 3'''
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	'''Question 5'''		'''Question 5'''

	TreeAnnotator is used to summarize the posterior sample of trees into a single representative tree. Compared with an ordinary phylogram or consensus tree, what additional information does this summary tree contain? Mention at least two specific annotations and explain briefly why each is useful.		TreeAnnotator is used to summarize the posterior sample of trees into a single representative tree. Compared with an ordinary phylogram or a simple consensus tree, what additional information does this summary tree contain? Mention at least two specific annotations visible in this tutorial, and explain briefly why each is useful.

	'''Question 6'''		'''Question 6'''
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	'''Question 8'''		'''Question 8'''

	Based on the relaxed-clock analysis, is there evidence for substantial rate variation among lineages? In your answer, state ~~what output~~ you ~~used~~ to assess this. Also comment on whether the main biological conclusion about introduction of yellow fever virus into the Americas changes or remains similar under the relaxed-clock model.		Based on the relaxed-clock analysis, is there evidence for substantial rate variation among lineages? In your answer, state which parameter in Tracer you inspected to assess this, and explain what kind of result would indicate little versus substantial rate variation. Also comment on whether the main biological conclusion about introduction of yellow fever virus into the Americas changes or remains similar under the relaxed-clock model.

Gorm at 10:39, 22 April 2026

2026-04-22T10:39:12Z

@@ Line 3: / Line 3: @@
 == Overview ==
-In this exercise we will explore how to use the software tool BEASTX to construct phylogenies based on molecular-clock models. In previous exercises we have worked with phylogenies where we did not have information about how fast sequences were evolving, and we therefore used the number of substitutions as branch lengths. When there ''is'' temporal information (e.g., fossils that can be used to date an internal node, or information about sampling-time for rapidly evolving sequences) we can instead use clock-based models. These models assume that sequences are evolving at a more or less constant rate, branch lengths are expressed in terms of time, and we can estimate times for internal nodes. Apart from being useful when the focus is on dating evolutionary events, time trees are also useful in that the clock model itself can lead to better inference of the phylogeny (essentially because it adds prior information to the problem, such that we dont have to infer all branch lengths only from limited amounts of sequence variation).
+In this exercise we will use the software package BEASTX to infer phylogenies under molecular-clock models.
-The main purpose with this exercise is to make you acquainted with BEASTX and to learn how to fit clock-models using either fossil data (by setting a prior on the date for internal nodes) or using so-called heterochronous data, i.e., sequences where the individual leaves have been sampled at different, known times, and where evolution is sufficiently rapid that we can estimate the parameters in a clock-model by seeing how much change has happened over time.
+In previous exercises, branch lengths were measured only in expected numbers of substitutions per site. In a clock-based analysis, genetic change is instead related to calendar time through a model of evolutionary rates. If temporal information is available, for example in the form of known sampling times for rapidly evolving sequences, this can be used to estimate both the rate of evolution and the times of internal nodes in the tree.
-For these tutorials you only need to report minimally: make a small report with a handful of uncommented screendumps showing your progress through the exercise. The important thing is that you get to be a bit familiar with the use of the program, such that you can use it in the mini project later.
+In this exercise we will focus on so-called heterochronous data, i.e., sequence data where the individual sequences were sampled at different known times. When evolution is sufficiently rapid, the amount of sequence change observed over these sampling times contains information about the evolutionary rate and about the timing of common ancestors.
-:* In the exercises below, you should simply follow the instructions on the tutorial pages.
+The main purpose of the exercise is:
-:* Depending on your operating system and on how you installed the software, you can start required programs either from the command line or by double clicking an app. The names of the executables that you will need for this exercise are:
+:* to become familiar with the BEASTX workflow
 :** beauti
 :** beast
@@ Line 17: / Line 25: @@
 :** figtree
-== Introduction to BEASTX ==
+== BEASTX tutorial ==
-:* Create a new directory for storing the results of this exercise:
+The tutorial then repeats the analysis using a relaxed lognormal clock. What is the difference between a strict clock and this relaxed-clock model? What extra biological possibility is the relaxed-clock model allowing for?
-== Prior selection and clock calibration using Influenza A data ==
+'''Question 8'''
-:* Open this link in a new tab: [https://taming-the-beast.org/tutorials/Prior-selection/ Prior selection and clock calibration using Influenza A data]
+Based on the relaxed-clock analysis, is there evidence for substantial rate variation among lineages? In your answer, state what output you used to assess this. Also comment on whether the main biological conclusion about introduction of yellow fever virus into the Americas changes or remains similar under the relaxed-clock model.

Gorm: /* Introduction to BEAST2 */

2026-04-22T09:33:52Z

Introduction to BEAST2

← Older revision		Revision as of 11:33, 22 April 2026
Line 17:		Line 17:
	:** figtree		:** figtree

	== Introduction to ~~BEAST2~~ ==		== Introduction to BEASTX ==

	:* Create a new directory for storing the results of this exercise:		:* Create a new directory for storing the results of this exercise:
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	:* Open this link in a new tab: [https://taming-the-beast.org/tutorials/Introduction-to-BEAST2/ Introduction to BEAST2]		:* Open this link in a new tab: [https://taming-the-beast.org/tutorials/Introduction-to-BEAST2/ Introduction to BEAST2]
	:* Follow instructions down to the optional part.		:* Follow instructions down to the optional part.
	:* '''Note:''' If you are running the ~~BEAST2~~ programs from the command line (not starting them by double clicking an app), then to get the graphical interface for ~~BEAST2~~ shown in figure 11 in the tutorial, you should start the program as follows:		:* '''Note:''' If you are running the BEASTX programs from the command line (not starting them by double clicking an app), then to get the graphical interface for BEASTX shown in figure 11 in the tutorial, you should start the program as follows:
	beast -options		beast -options

Gorm: /* Overview */

2026-04-22T09:33:17Z

Overview

← Older revision		Revision as of 11:33, 22 April 2026
Line 3:		Line 3:
	== Overview ==		== Overview ==

	In this exercise we will explore how to use the software tool ~~BEAST2~~ to construct phylogenies based on molecular-clock models. In previous exercises we have worked with phylogenies where we did not have information about how fast sequences were evolving, and we therefore used the number of substitutions as branch lengths. When there ''is'' temporal information (e.g., fossils that can be used to date an internal node, or information about sampling-time for rapidly evolving sequences) we can instead use clock-based models. These models assume that sequences are evolving at a more or less constant rate, branch lengths are expressed in terms of time, and we can estimate times for internal nodes. Apart from being useful when the focus is on dating evolutionary events, time trees are also useful in that the clock model itself can lead to better inference of the phylogeny (essentially because it adds prior information to the problem, such that we dont have to infer all branch lengths only from limited amounts of sequence variation).		In this exercise we will explore how to use the software tool BEASTX to construct phylogenies based on molecular-clock models. In previous exercises we have worked with phylogenies where we did not have information about how fast sequences were evolving, and we therefore used the number of substitutions as branch lengths. When there ''is'' temporal information (e.g., fossils that can be used to date an internal node, or information about sampling-time for rapidly evolving sequences) we can instead use clock-based models. These models assume that sequences are evolving at a more or less constant rate, branch lengths are expressed in terms of time, and we can estimate times for internal nodes. Apart from being useful when the focus is on dating evolutionary events, time trees are also useful in that the clock model itself can lead to better inference of the phylogeny (essentially because it adds prior information to the problem, such that we dont have to infer all branch lengths only from limited amounts of sequence variation).

	The main purpose with this exercise is to make you acquainted with ~~BEAST2~~ and to learn how to fit clock-models using either fossil data (by setting a prior on the date for internal nodes) or using so-called heterochronous data, i.e., sequences where the individual leaves have been sampled at different, known times, and where evolution is sufficiently rapid that we can estimate the parameters in a clock-model by seeing how much change has happened over time.		The main purpose with this exercise is to make you acquainted with BEASTX and to learn how to fit clock-models using either fossil data (by setting a prior on the date for internal nodes) or using so-called heterochronous data, i.e., sequences where the individual leaves have been sampled at different, known times, and where evolution is sufficiently rapid that we can estimate the parameters in a clock-model by seeing how much change has happened over time.

	For these tutorials you only need to report minimally: make a small report with a handful of uncommented screendumps showing your progress through the exercise. The important thing is that you get to be a bit familiar with the use of the program, such that you can use it in the mini project later.		For these tutorials you only need to report minimally: make a small report with a handful of uncommented screendumps showing your progress through the exercise. The important thing is that you get to be a bit familiar with the use of the program, such that you can use it in the mini project later.

Gorm: /* Overview */

2025-04-23T06:53:25Z

Overview

← Older revision		Revision as of 08:53, 23 April 2025
Line 10:		Line 10:

	:* In the exercises below, you should simply follow the instructions on the tutorial pages.		:* In the exercises below, you should simply follow the instructions on the tutorial pages.
	:* In the ~~virtual box~~ you ~~should~~ start programs from the command line, by ~~simply writing the name of the executable~~. The names of the executables that you will need for this exercise are:		:* Depending on your operating system and on how you installed the software, you can start required programs either from the command line or by double clicking an app. The names of the executables that you will need for this exercise are:
	:** beauti		:** beauti
	:** beast		:** beast

Gorm: /* Introduction to BEAST2 */

2024-04-17T06:32:37Z

Introduction to BEAST2

← Older revision		Revision as of 08:32, 17 April 2024
Line 25:		Line 25:
	:* Open this link in a new tab: [https://taming-the-beast.org/tutorials/Introduction-to-BEAST2/ Introduction to BEAST2]		:* Open this link in a new tab: [https://taming-the-beast.org/tutorials/Introduction-to-BEAST2/ Introduction to BEAST2]
	:* Follow instructions down to the optional part.		:* Follow instructions down to the optional part.
	:* '''Note:''' To get the graphical interface for BEAST2 shown in figure 11 in the tutorial, you should start the program as follows:		:* '''Note:''' If you are running the BEAST2 programs from the command line (not starting them by double clicking an app), then to get the graphical interface for BEAST2 shown in figure 11 in the tutorial, you should start the program as follows:
	beast -options		beast -options

WikiSysop: Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Overview == In this exercise we will explore how to use the software tool BEAST2 to construct phylogenies based on molecular-clock models. In previous exercises we have worked with phylogenies where we did not have information about how fast sequences were evolving, and we therefore used the number of substitutions as branch lengths. When the..."

2024-03-19T13:48:12Z

Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Overview == In this exercise we will explore how to use the software tool BEAST2 to construct phylogenies based on molecular-clock models. In previous exercises we have worked with phylogenies where we did not have information about how fast sequences were evolving, and we therefore used the number of substitutions as branch lengths. When the..."

New page

This exercise is part of the course [[22115_-_Computational_Molecular_Evolution|Computational Molecular Evolution (22115)]].

== Overview ==

In this exercise we will explore how to use the software tool BEAST2 to construct phylogenies based on molecular-clock models. In previous exercises we have worked with phylogenies where we did not have information about how fast sequences were evolving, and we therefore used the number of substitutions as branch lengths. When there ''is'' temporal information (e.g., fossils that can be used to date an internal node, or information about sampling-time for rapidly evolving sequences) we can instead use clock-based models. These models assume that sequences are evolving at a more or less constant rate, branch lengths are expressed in terms of time, and we can estimate times for internal nodes. Apart from being useful when the focus is on dating evolutionary events, time trees are also useful in that the clock model itself can lead to better inference of the phylogeny (essentially because it adds prior information to the problem, such that we dont have to infer all branch lengths only from limited amounts of sequence variation).

The main purpose with this exercise is to make you acquainted with BEAST2 and to learn how to fit clock-models using either fossil data (by setting a prior on the date for internal nodes) or using so-called heterochronous data, i.e., sequences where the individual leaves have been sampled at different, known times, and where evolution is sufficiently rapid that we can estimate the parameters in a clock-model by seeing how much change has happened over time.

For these tutorials you only need to report minimally: make a small report with a handful of uncommented screendumps showing your progress through the exercise. The important thing is that you get to be a bit familiar with the use of the program, such that you can use it in the mini project later.

:* In the exercises below, you should simply follow the instructions on the tutorial pages.
:* In the virtual box you should start programs from the command line, by simply writing the name of the executable. The names of the executables that you will need for this exercise are:
:** beauti
:** beast
:** tracer
:** treeannotator
:** figtree

== Introduction to BEAST2 ==

:* Create a new directory for storing the results of this exercise:
cd /path/to/molevol
mkdir bayes2
cd bayes2
:* Open this link in a new tab: [https://taming-the-beast.org/tutorials/Introduction-to-BEAST2/ Introduction to BEAST2]
:* Follow instructions down to the optional part.
:* '''Note:''' To get the graphical interface for BEAST2 shown in figure 11 in the tutorial, you should start the program as follows:
beast -options

== Prior selection and clock calibration using Influenza A data ==

:* Open this link in a new tab: [https://taming-the-beast.org/tutorials/Prior-selection/ Prior selection and clock calibration using Influenza A data]
:* '''NOTE:''' Only do the part about '''heterochronous''' data (not the homochronous part, although you can if you want to)