22115 - Computational Molecular Evolution - Revision history

Gorm: /* Week 7 (March 18): Bayesian inference of phylogeny */

2026-03-17T21:36:21Z

Week 7 (March 18): Bayesian inference of phylogeny

← Older revision		Revision as of 23:36, 17 March 2026
Line 132:		Line 132:
	:* [[Media:MTN122.pdf\|An Introduction to Bayesian Statistics Without Using Equations]]		:* [[Media:MTN122.pdf\|An Introduction to Bayesian Statistics Without Using Equations]]
	:* [http://www.nature.com/nbt/journal/v22/n9/pdf/nbt0904-1177.pdf Background reading: "What is Bayesian statistics?"]		:* [http://www.nature.com/nbt/journal/v22/n9/pdf/nbt0904-1177.pdf Background reading: "What is Bayesian statistics?"]
	:* [~~http~~://~~rsta~~.~~royalsocietypublishing.org~~/~~content~~/~~roypta~~/~~361~~/~~1813/2681.full~~.pdf Background reading: "Bayesian computation: a statistical revolution"]		:* [https://gwern.net/doc/statistics/bayes/2003-brooks.pdf Background reading: "Bayesian computation: a statistical revolution"]

	:; Computer exercise		:; Computer exercise

Gorm: /* Week 7 (March 18): Bayesian inference of phylogeny */

2026-03-17T21:34:07Z

Week 7 (March 18): Bayesian inference of phylogeny

← Older revision		Revision as of 23:34, 17 March 2026
Line 130:		Line 130:
	:* [https://teaching.healthtech.dtu.dk/material/22115/Handout.class08.pdf Handout exercise: Bayesian estimation of model parameter value]		:* [https://teaching.healthtech.dtu.dk/material/22115/Handout.class08.pdf Handout exercise: Bayesian estimation of model parameter value]
	:* [https://teaching.healthtech.dtu.dk/material/22115/Slides_week5.pdf Slides, week 7]		:* [https://teaching.healthtech.dtu.dk/material/22115/Slides_week5.pdf Slides, week 7]
	:* [~~https~~:~~//teaching.healthtech.dtu.dk/material/22115/~~MTN122.pdf\| An Introduction to Bayesian Statistics Without Using Equations]		:* [[Media:MTN122.pdf\|An Introduction to Bayesian Statistics Without Using Equations]]
	:* [http://www.nature.com/nbt/journal/v22/n9/pdf/nbt0904-1177.pdf Background reading: "What is Bayesian statistics?"]		:* [http://www.nature.com/nbt/journal/v22/n9/pdf/nbt0904-1177.pdf Background reading: "What is Bayesian statistics?"]
	:* [http://rsta.royalsocietypublishing.org/content/roypta/361/1813/2681.full.pdf Background reading: "Bayesian computation: a statistical revolution"]		:* [http://rsta.royalsocietypublishing.org/content/roypta/361/1813/2681.full.pdf Background reading: "Bayesian computation: a statistical revolution"]

Gorm at 11:04, 11 February 2026

2026-02-11T11:04:46Z

← Older revision		Revision as of 13:04, 11 February 2026
Line 1:		Line 1:
	; Overview [[File:Darwin logo2 medium.png \|right\|border\|550px]]		; Overview [[File:Darwin logo2 medium.png \|right\|border\|550px]]
	: This page contains links to video lectures, computer exercises, and other material for the course [https://kurser.dtu.dk/course/22115 22115 - Computational Molecular Evolution], which is part of the [https://www.dtu.dk/english/education/msc/programmes/~~systems_biology~~ MSc in Bioinformatics and Systems Biology] at the [https://www.dtu.dk/english Technical University of Denmark]. The course is taught by Professor Anders Gorm Pedersen, [https://www.healthtech.dtu.dk/english/Research/Research-Sections/Section-Bioinformatics Section for Bioinformatics], [https://www.healthtech.dtu.dk/english Department of Health Technology].		: This page contains links to video lectures, computer exercises, and other material for the course [https://kurser.dtu.dk/course/22115 22115 - Computational Molecular Evolution], which is part of the [https://www.dtu.dk/english/education/graduate/msc-programmes/bioinformatics MSc in Bioinformatics and Systems Biology] at the [https://www.dtu.dk/english Technical University of Denmark]. The course is taught by Professor Anders Gorm Pedersen, [https://www.healthtech.dtu.dk/english/Research/Research-Sections/Section-Bioinformatics Section for Bioinformatics], [https://www.healthtech.dtu.dk/english Department of Health Technology].

	: The main goal of this course is to give an introduction to theory and algorithms in the field of computational molecular evolution. We will cover basic evolutionary theory (common descent, natural selection, genetic drift, models of growth and selection), and the main types of algorithms used for constructing and analyzing phylogenetic trees (parsimony, distance based methods, maximum likelihood methods, and Bayesian inference). We will also discuss the role of statistical modeling in science more generally		: The main goal of this course is to give an introduction to theory and algorithms in the field of computational molecular evolution. We will cover basic evolutionary theory (common descent, natural selection, genetic drift, models of growth and selection), and the main types of algorithms used for constructing and analyzing phylogenetic trees (parsimony, distance based methods, maximum likelihood methods, and Bayesian inference). We will also discuss the role of statistical modeling in science more generally

Gorm: /* Computer setup */

2026-02-03T10:14:00Z

Computer setup

← Older revision		Revision as of 12:14, 3 February 2026
Line 15:		Line 15:
	:* [[MacOS software installation]]		:* [[MacOS software installation]]
	<!-- :* [[Notes on using MacOS for exercises]] '''UNDER CONSTRUCTION''' -->		<!-- :* [[Notes on using MacOS for exercises]] '''UNDER CONSTRUCTION''' -->
	~~<!--~~

	===Windows===		===Windows===

Gorm: /* Computer setup */

2026-02-03T10:13:36Z

Computer setup

← Older revision		Revision as of 12:13, 3 February 2026
Line 12:		Line 12:
	=='''Computer setup'''==		=='''Computer setup'''==

	===~~Linux~~===		===MacOS===
	:* [[~~Linux~~ software installation]]		:* [[MacOS software installation]]
	<!-- :* [[Notes on using ~~Linux~~ for exercises]] '''UNDER CONSTRUCTION''' -->		<!-- :* [[Notes on using MacOS for exercises]] '''UNDER CONSTRUCTION''' -->
			<!--

	===Windows===		===Windows===
Line 20:		Line 21:
	<!-- :* [[Windows software installation - Old Version]] -->		<!-- :* [[Windows software installation - Old Version]] -->

	===~~MacOS~~===		===Linux===
	:* [[~~MacOS~~ software installation]]		:* [[Linux software installation]]
	<!-- :* [[Notes on using ~~MacOS~~ for exercises]] '''UNDER CONSTRUCTION''' ~~-->~~		<!-- :* [[Notes on using Linux for exercises]] '''UNDER CONSTRUCTION''' -->
	~~<!--~~
	~~===VirtualBox===~~
	~~:* Use this only if you can't install natively on MacOS, Windows, or Linux. Runs a virtual Linux on top of your own OS.~~
	~~:* [[VirtualBox installation]]~~
	~~:* [[Notes on using VirtualBox for exercises]]~~
	-->

	== '''Lecture Schedule''' ==		== '''Lecture Schedule''' ==

Gorm: /* Computer setup */

2026-02-02T09:49:37Z

Computer setup

← Older revision		Revision as of 11:49, 2 February 2026
Line 18:		Line 18:
	===Windows===		===Windows===
	:* [[Windows software installation]]		:* [[Windows software installation]]
	:* [[Windows software installation - Old Version]]		<!-- :* [[Windows software installation - Old Version]] -->

	===MacOS===		===MacOS===

Gorm: /* Windows */

2026-02-02T09:15:04Z

Windows

← Older revision		Revision as of 11:15, 2 February 2026
Line 18:		Line 18:
	===Windows===		===Windows===
	:* [[Windows software installation]]		:* [[Windows software installation]]
	~~<!--~~:* [[~~Notes on using~~ Windows ~~for exercises~~]] ~~'''UNDER CONSTRUCTION''' -->~~		:* [[Windows software installation - Old Version]]

	===MacOS===		===MacOS===

Gorm: /* Lecture Schedule */

2026-01-31T10:10:52Z

Lecture Schedule

← Older revision		Revision as of 12:10, 31 January 2026
Line 34:		Line 34:
	:([[27615 Previous course programs\|Course programs, previous years]])		:([[27615 Previous course programs\|Course programs, previous years]])

	===Week 1 (February 5): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation===		===Week 1 (February 4): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation===

	:; Online lectures		:; Online lectures
Line 52:		Line 52:
	----		----

	===Week 2 (February 12): Neutral mutations and genetic drift. Tree reconstruction by parsimony===		===Week 2 (February 11): Neutral mutations and genetic drift. Tree reconstruction by parsimony===

	:; Online lectures		:; Online lectures
Line 72:		Line 72:
	----		----

	===Week 3 (February 19): Consensus trees. Distance matrix methods===		===Week 3 (February 18): Consensus trees. Distance matrix methods===

	:; Online lectures		:; Online lectures
Line 91:		Line 91:
	----		----

	===Week 4+5 (February 26 + March 5): Mini project 1===		===Week 4+5 (February 25 + March 4): Mini project 1===

	<!--		<!--
Line 108:		Line 108:
	----		----

	===Week 6 (March 12): Models of sequence evolution. Likelihood methods===		===Week 6 (March 11): Models of sequence evolution. Likelihood methods===

	:; Online lectures		:; Online lectures
Line 127:		Line 127:
	----		----

	===Week 7 (March 19): Bayesian inference of phylogeny===		===Week 7 (March 18): Bayesian inference of phylogeny===

	:; Online lectures		:; Online lectures
Line 145:		Line 145:
	----		----

	===Week 8+9 (March 26 + April 2): Mini project 2===		===Week 8+9 (March 25 + April 8): Mini project 2===

	<!--		<!--
Line 156:		Line 156:
	----		----

	===Week 10 (April 9): Model Selection===		===Week 10 (April 15): Model Selection===

	:; Online lectures		:; Online lectures
Line 172:		Line 172:
	----		----

	===Week 11 (April 23): Bayesian Phylogenetics, Part 2 ===		===Week 11 (April 22): Bayesian Phylogenetics, Part 2 ===
	:; Course material		:; Course material
	:* [https://www.researchgate.net/publication/319965471_A_biologist%27s_guide_to_Bayesian_phylogenetic_analysis A biologist’s guide to Bayesian phylogenetic analysis]		:* [https://www.researchgate.net/publication/319965471_A_biologist%27s_guide_to_Bayesian_phylogenetic_analysis A biologist’s guide to Bayesian phylogenetic analysis]
Line 186:		Line 186:
	----		----

	===Week 12 + 13 (April 30 + May 7): Mini project 3: Final exam===		===Week 12 + 13 (April 20 + May 6): Mini project 3: Final exam===

	'''Details will follow'''		'''Details will follow'''

	----		----

Gorm: /* Week 11 (April 23): Bayesian Phylogenetics, Part 2 */

2025-04-30T20:52:42Z

Week 11 (April 23): Bayesian Phylogenetics, Part 2

← Older revision		Revision as of 22:52, 30 April 2025
Line 177:		Line 177:
	:* [https://beast.community/analysing_beast_output Analysing BEAST output using Tracer]		:* [https://beast.community/analysing_beast_output Analysing BEAST output using Tracer]
	:* [https://beast.community/tracer_convergence Identifying convergence problems using Tracer]		:* [https://beast.community/tracer_convergence Identifying convergence problems using Tracer]
	:* [https://taming-the-beast.org/tutorials/Troubleshooting-convergence-issues/ ~~Post-processing and improving performance~~]		:* [https://taming-the-beast.org/tutorials/Troubleshooting-initialization-issues/ Troubleshooting initialization issues]
			:* [https://taming-the-beast.org/tutorials/Troubleshooting-convergence-issues/ Troubleshooting convergence issues]

	:; Computer exercise		:; Computer exercise

Gorm: /* Week 11 (April 23): Bayesian Phylogenetics, Part 2 */

2025-04-30T20:50:16Z

Week 11 (April 23): Bayesian Phylogenetics, Part 2

← Older revision		Revision as of 22:50, 30 April 2025
Line 177:		Line 177:
	:* [https://beast.community/analysing_beast_output Analysing BEAST output using Tracer]		:* [https://beast.community/analysing_beast_output Analysing BEAST output using Tracer]
	:* [https://beast.community/tracer_convergence Identifying convergence problems using Tracer]		:* [https://beast.community/tracer_convergence Identifying convergence problems using Tracer]
	:* [https://taming-the-beast.org/tutorials/Troubleshooting/ Post-processing and improving performance]		:* [https://taming-the-beast.org/tutorials/Troubleshooting-convergence-issues/ Post-processing and improving performance]

	:; Computer exercise		:; Computer exercise