Difference between revisions of "Phylogenetics: Syllabus"
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|rowspan="2" valign="top"|[[Image:Adiantum.png|200px]] | |rowspan="2" valign="top"|[[Image:Adiantum.png|200px]] | ||
− | |<span style="font-size: x-large">EEB | + | |<span style="font-size: x-large">EEB 349: Phylogenetics</span> |
|- | |- | ||
− | | '''Lectures:''' | + | | '''Lectures:''' MW 11-12:15 (CUE 320)<br/>'''Lab:''' M 1-3 (TLS 477)<br/>'''Lecture Instructor:''' [mailto:paul.lewis@uconn.edu Paul O. Lewis]<br/>'''Lab Instructor:''' [mailto:maxi.polihronakis@uconn.edu Maxi Polihronakis] |
|} | |} | ||
== Lecture Topics == | == Lecture Topics == | ||
− | The following syllabus is tentative and probably will change without notice numerous times during the semester. Also, the content of linked presentations may change as well (so if you intend to print out lectures before class, do so as late as possible). Changes made after lectures are given will primarily reflect correction of typographical errors. | + | The following syllabus is tentative and probably will change without notice numerous times during the semester. Also, the content of linked presentations may change as well (so if you intend to print out lectures before class, do so as late as possible). Changes made after lectures are given will primarily reflect correction of typographical errors. All content linked to this page is copyright © 2007 by Paul O. Lewis. |
{| border="1" | {| border="1" | ||
|- | |- | ||
| Day || Lecture || Lab/Homework | | Day || Lecture || Lab/Homework | ||
− | |||
− | |||
− | |||
− | |||
|- | |- | ||
− | | | + | | Wed., Jan. 17 |
− | | '''Introduction | + | | '''Introduction''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Introduction_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Introduction_6perpage.pdf}}<br/>Significance, history, terminology |
− | | | + | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw1_TreeFromSplits.pdf}} Tree from splits |
|- | |- | ||
− | | | + | | Mon., Jan. 22 |
− | | ''' | + | | '''Tree thinking''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TreeThinking_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TreeThinking_6perpage.pdf}}<br/>Rooted/unrooted, ultrametric/free, paralogy/orthology, lineage sorting, "basal" lineages |
− | | | + | | {{EEB349lab|{{SERVER}}/people/plewis/courses/phylogenetics/labs/paupnexus.html}} Nexus data files |
|- | |- | ||
− | | | + | | Wed., Jan. 24 |
− | | ''' | + | | '''Consensus trees''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Consensus_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Consensus_6perpage.pdf}} '''Parsimony''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Parsimony_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Parsimony_6perpage.pdf}}<br/> |
− | | | + | Camin-Sokal, Wagner, Fitch, Dollo, transversion, generalized, step-matrix |
+ | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw2_Parsimony.pdf}} Parsimony | ||
|- | |- | ||
− | | | + | | Mon., Jan. 29 |
− | | ''' | + | | '''Polyphyly vs. Paraphyly Revisited''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TreeThinking2_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TreeThinking2_6perpage.pdf}} '''Searching''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Searching_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Searching_6perpage.pdf}}<br/>Exhaustive, branch-and-bound, star decomposition, stepwise addition, heuristic, genetic algorithms |
− | | | + | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Parsimony_Lab}} Searching |
|- | |- | ||
− | | | + | | Wed., Jan. 31 |
− | | ''' | + | | '''Distances''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Distances_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Distances_6perpage.pdf}}<br/>Least squares criterion, minimum evolution criterion, split decomposition, quartet puzzling, DCM, NJ |
− | | | + | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw3_Distances.pdf}} Distances |
|- | |- | ||
− | | | + | | Mon., Feb. 5 |
− | | ''' | + | | '''Substitution models''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Models_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Models_6perpage.pdf}}<br/>Transition probability, instantaneous rates, JC69 model, K2P model, F81 model, F84 model, HKY85 model, GTR model |
− | | | + | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Distances_Lab}} Distance methods |
|- | |- | ||
− | | | + | | Wed., Feb. 7 |
− | | ''' | + | | '''Maximum likelihood''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Likelihood_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Likelihood_6perpage.pdf}}<br/>Likelihood of a DNA sequence, likelihood of a pair of sequences, parameter estimation (MLEs), likelihood of a tree, likelihood ratio test, simulation |
− | | | + | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw4_Likelihood.pdf}} Likelihood |
|- | |- | ||
− | | | + | | Mon., Feb. 12 |
− | | ''' | + | | '''Rate heterogeneity''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/RateHeterogeneity_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/RateHeterogeneity_6perpage.pdf}} '''Addendum''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/RateHeterogeneityAddendum.pdf}}<br/>Proportion of invariable sites, discrete gamma, site-specific rates |
− | | | + | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Likelihood_Lab}} Likelihood |
|- | |- | ||
− | | | + | | Wed., Feb. 14 |
− | | ''' | + | | '''*** Snow day: no class today ***''' (but do begin working on homework 5) |
− | | | + | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw5_RateHet.pdf}} Rate Het. |
|- | |- | ||
− | | | + | | Mon., Feb. 19 |
− | | ''' | + | | '''Secondary structure (stem) models''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/StemModels_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/StemModels_6perpage.pdf}} <span id="codon_models">'''Codon models'''</span> {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CodonModels_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CodonModels_6perpage.pdf}}<br/>RNA stem/loop structure, compensatory substitutions, stem models, nonsynonymous vs. synonymous rates, codon models |
− | | | + | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Bioinformatics_Cluster}} Using the cluster |
|- | |- | ||
− | | | + | | Wed., Feb. 21 |
− | | ''' | + | | '''Bootstrapping''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Bootstrapping_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Bootstrapping_6perpage.pdf}} '''Bremer support''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Bremer_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Bremer_6perpage.pdf}} '''Topology tests''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TopologyTests_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TopologyTests_6perpage.pdf}}<br/>Bootstrapping, Bremer support, KH test, SH test, SOWH test |
− | | | + | | No homework assignment this week |
|- | |- | ||
− | | | + | | Mon., Feb. 26 |
− | | ''' | + | | '''Simulation''' (updated) {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Simulation_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Simulation_6perpage.pdf}} '''Long branch attraction''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/LBA_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/LBA_6perpage.pdf}} '''Model selection, part I''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/LRT_AIC_BIC_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/LRT_AIC_BIC_6perpage.pdf}} <br/>Stochastic simulation, statistical consistency, long branch attraction, long branch repulsion, likelihood ratio tests, Akaike Information criterion (AIC), Bayesian Information Criterion (BIC) |
− | | | + | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_HyPhy_Lab}} Hy-Phy |
|- | |- | ||
− | | | + | | Wed., Feb. 28 |
− | |''' | + | | '''Data partitioning''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Partitioning_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Partitioning_6perpage.pdf}} '''Expected substitutions''' (updated) {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/ExpectedSubstitutions_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/ExpectedSubstitutions_6perpage.pdf}} <br/>ILD test for combinability, using different model for each partition |
− | | ''' | + | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw6_Simulation.pdf}} Simulation |
|- | |- | ||
− | | | + | | Mon., Mar. 5 |
− | | '''Spring break''' | + | | '''Spring break'''<br/>no class |
− | | no class | + | | no class |
|- | |- | ||
− | | | + | | Wed., Mar. 7 |
| '''Spring break''' | | '''Spring break''' | ||
| no class | | no class | ||
|- | |- | ||
− | | | + | | Mon., Mar. 12 |
− | | ''' | + | | '''Bayes primer''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianIntro_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianIntro_6perpage.pdf}} <br/>Conditional/joint probabilities, Bayes rule, prior vs. posterior distributions, probability mass vs. probability density, Markov chain Monte Carlo (start) |
− | | | + | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Modeltest_Lab}} ModelTest/Gamma dist. |
+ | |- | ||
+ | | Wed., Mar. 14 | ||
+ | | '''Bayesian phylogenetics''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianPhylogenetics_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianPhylogenetics_6perpage.pdf}} <br/>MCMC (continued), heated chains, choosing prior distributions | ||
+ | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw7_MCMC.pdf}} MCMC | ||
+ | |- | ||
+ | | Mon., Mar. 19 | ||
+ | | '''Prior distributions''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/PriorDistributions_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/PriorDistributions_6perpage.pdf}}<br/>Summarizing posterior distributions, commonly-used prior distributions, problem priors, reversible-jump MCMC, star tree paradox | ||
+ | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_MrBayes_Lab}} MrBayes | ||
+ | |- | ||
+ | | Wed., Mar. 21 | ||
+ | | '''Confidence intervals''' (follow-up on last lecture) {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/ConfidenceIntervals_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/ConfidenceIntervals_6perpage.pdf}} '''Model Selection, part II''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelection_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelection_6perpage.pdf}}<br/>Bayes factors, posterior predictive approaches to model selection | ||
+ | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw8_LocalMove.pdf}} LOCAL move | ||
+ | |- | ||
+ | | Mon., Mar. 26 | ||
+ | | '''Model Selection, part II (4 extra slides)''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelExtra_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelExtra_6perpage.pdf}} | ||
+ | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Mesquite_Lab}} Mesquite | ||
+ | |- | ||
+ | | Wed., Mar. 28 | ||
+ | | '''Ancestral Character States''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/AncStates_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/AncStates_6perpage.pdf}} <br/>Parsimony approach, ML approach, empirical Bayes approach | ||
+ | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw9_AncStates.pdf}} Anc. states | ||
|- | |- | ||
− | | | + | | Mon., Apr. 2 |
− | | | + | | No lecture today |
− | | | + | | No lab today |
|- | |- | ||
− | | | + | | Wed., Apr. 4 |
− | | | + | | '''Models for discrete morphological data''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/MorphModels_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/MorphModels_6perpage.pdf}} <br/>DNA sequences vs. morphological characters, Symmetric vs. asymmetric 2-state models, Mk model, estimating morphological branch lengths |
− | | | + | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw10_CondVar.pdf}} Mk model |
|- | |- | ||
− | | | + | | Mon., Apr. 9 |
− | | | + | | '''Discrete Character Correlation''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CorrelatedEvolution_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CorrelatedEvolution_6perpage.pdf}} |
− | | | + | '''Continuous Character Correlation''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/IndependentContrasts_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/IndependentContrasts_6perpage.pdf}} <br/>Pagel's likelihood ratio test, Felsenstein's threshhold model, Felsenstein's independent contrasts |
+ | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Morphology_and_Partitioning_in_MrBayes}} Partitioning/Morphology | ||
|- | |- | ||
− | | | + | | Wed., Apr. 11 |
− | | ''' | + | | '''Stochastic Character Mapping''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/MorphMappingSIMMAP_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/MorphMappingSIMMAP_6perpage.pdf}} <br/>Concentrated changes test, stochastic mapping for estimating ancestral states and character correlation, SIMMAP demo |
− | | | + | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw11_MorphMap.pdf}} Mapping |
|- | |- | ||
− | | | + | | Mon., Apr. 16 |
− | | ''' | + | | '''Stochastic Character Mapping''' (finish) |
− | | | + | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_BayesTraits_Lab}} BayesTraits |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
|- | |- | ||
− | | | + | | Wed., Apr. 18 |
− | | ''' | + | | '''Divergence Time Estimation''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/DivergenceTimes_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/DivergenceTimes_6perpage.pdf}} <br/>Non-parametric rate smoothing, penalized likelihood, cross-validation, Bayesian approaches |
− | | | + | | Read chapter and paper for Apr. 25 |
− | + | ||
− | + | ||
− | + | ||
− | | | + | |
|- | |- | ||
− | | | + | | Mon., Apr. 23 |
− | | ''' | + | | '''Inferring key innovations''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/KeyInnovations_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/KeyInnovations_6perpage.pdf}} '''The Remainder''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Conclusion2007_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Conclusion2007_6perpage.pdf}}<br>Key innovations, clade contrast approach, stochastic mapping method, what ''was'' and ''was not'' covered in this course (also course evaluations) |
− | | | + | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_r8s_Lab}} r8s |
− | + | ||
− | + | ||
− | + | ||
− | | | + | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | | | + | |
− | | | + | |
− | + | ||
− | + | ||
|- | |- | ||
− | | Wed., | + | | Wed., Apr. 25 |
− | | | + | | '''Alignment''' (guest lecture by Karl Kjer) {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Alignment_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Alignment_6perpage.pdf}} Reading: Chapter {{pdf|{{SERVER}}/people/plewis/courses/phylogenetics/restricted/Alignmentchapter_near_final.pdf}} Paper {{pdf|{{SERVER}}/people/plewis/courses/phylogenetics/restricted/Kjer_Gillespie_Ober_2007_SystBiol_56_133-146.pdf}}<br/>Toner-saver version of lecture (note: some details may be obscured by conversion to pure black and white): {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Alignment_1perpage_bw.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Alignment_6perpage_bw.pdf}} |
− | | | + | | No homework today |
|} | |} | ||
Line 146: | Line 140: | ||
This course is designed to give you the background you need to understand and critically evaluate phylogenetic analyses described in current primary literature, and to design appropriate phylogenetic analyses to address your own research questions. | This course is designed to give you the background you need to understand and critically evaluate phylogenetic analyses described in current primary literature, and to design appropriate phylogenetic analyses to address your own research questions. | ||
− | + | Unlike many graduate courses, you will not spend a lot of time reading papers in this course. Instead, you will spend time using state-of-the-art software tools and doing homework assignments designed to ensure that you understand the output of the programs. | |
There is a [http://evolution.genetics.washington.edu/phylip/software.html confusing diversity of programs] these days for performing phylogenetic analyses. We will concentrate on only a few so that you will know how to use these well by the end of the course. | There is a [http://evolution.genetics.washington.edu/phylip/software.html confusing diversity of programs] these days for performing phylogenetic analyses. We will concentrate on only a few so that you will know how to use these well by the end of the course. | ||
Line 156: | Line 150: | ||
== Labs == | == Labs == | ||
− | The laboratory section of this course consist of tutorials that you work through at your own pace | + | The laboratory section of this course is held in the MacCarthy computer lab on the fourth floor of Torrey Life Science (TLS 477). The labs will consist of tutorials that you work through at your own pace |
== Homeworks == | == Homeworks == | ||
− | Your grade will be based on | + | Your grade will be largely based on '''homework''' assignments, one of which will be assigned (nearly) every week. These homework assignments should be treated as if they were take-home, open-book exams. You may therefore consult with either me or the TA for the course, but not with fellow students when working on the homeworks. |
== Projects == | == Projects == | ||
− | In addition to homeworks, you will prepare a '''term paper''' to be due the last week of the course. There is a lot of flexibility in the nature of the term paper. If you have data of your own, you may decide to write a paper describing a phylogenetic analysis of these data, using appropriate methods learned during the course. If you are not yet at the stage of your graduate career where you have data of your own, you can do a thorough re-analysis of an existing data set. Finally, it is ok to simply write a review paper describing a particular topic in phylogenetics in depth. Please get my approval of your chosen topic before doing extensive work on your paper. | + | In addition to homeworks, you will prepare a '''term paper''' to be due the last week of the course. There is a lot of flexibility in the nature of the term paper. If you have data of your own, you may decide to write a paper describing a phylogenetic analysis of these data, using appropriate methods learned during the course. If you are not yet at the stage of your graduate career where you have data of your own, you can do a thorough re-analysis of an existing data set. Finally, it is ok to simply write a review paper describing a particular topic in phylogenetics in depth. If you choose this route, I will encourage you to write a paper suitable for contribution to [http://en.wikipedia.org/wiki/Main_Page Wikipedia] (this way, your efforts will survive the course and benefit the broader community). Please get my approval of your chosen topic before doing extensive work on your paper. |
== Links == | == Links == | ||
Line 174: | Line 168: | ||
* [http://www.hyphy.org/ HyPhy] | * [http://www.hyphy.org/ HyPhy] | ||
* [http://mesquiteproject.org/mesquite/mesquite.html Mesquite] | * [http://mesquiteproject.org/mesquite/mesquite.html Mesquite] | ||
− | * [http:// | + | * [http://evolve.zoo.ox.ac.uk/beast/ Beast] |
* [http://evolve.zoo.ox.ac.uk/software.html?id=tracer Tracer] | * [http://evolve.zoo.ox.ac.uk/software.html?id=tracer Tracer] | ||
* [http://taxonomy.zoology.gla.ac.uk/rod/treeview.html TreeView] | * [http://taxonomy.zoology.gla.ac.uk/rod/treeview.html TreeView] |
Revision as of 21:14, 12 January 2011
EEB 349: Phylogenetics | |
Lectures: MW 11-12:15 (CUE 320) Lab: M 1-3 (TLS 477) Lecture Instructor: Paul O. Lewis Lab Instructor: Maxi Polihronakis |
Lecture Topics
The following syllabus is tentative and probably will change without notice numerous times during the semester. Also, the content of linked presentations may change as well (so if you intend to print out lectures before class, do so as late as possible). Changes made after lectures are given will primarily reflect correction of typographical errors. All content linked to this page is copyright © 2007 by Paul O. Lewis.
Goals of this course
This course is designed to give you the background you need to understand and critically evaluate phylogenetic analyses described in current primary literature, and to design appropriate phylogenetic analyses to address your own research questions.
Unlike many graduate courses, you will not spend a lot of time reading papers in this course. Instead, you will spend time using state-of-the-art software tools and doing homework assignments designed to ensure that you understand the output of the programs.
There is a confusing diversity of programs these days for performing phylogenetic analyses. We will concentrate on only a few so that you will know how to use these well by the end of the course.
Textbook
No textbook is required for this course, although you might find Joe Felsenstein's 2004 book "Inferring Phylogenies" (published by Sinauer) useful.
Labs
The laboratory section of this course is held in the MacCarthy computer lab on the fourth floor of Torrey Life Science (TLS 477). The labs will consist of tutorials that you work through at your own pace
Homeworks
Your grade will be largely based on homework assignments, one of which will be assigned (nearly) every week. These homework assignments should be treated as if they were take-home, open-book exams. You may therefore consult with either me or the TA for the course, but not with fellow students when working on the homeworks.
Projects
In addition to homeworks, you will prepare a term paper to be due the last week of the course. There is a lot of flexibility in the nature of the term paper. If you have data of your own, you may decide to write a paper describing a phylogenetic analysis of these data, using appropriate methods learned during the course. If you are not yet at the stage of your graduate career where you have data of your own, you can do a thorough re-analysis of an existing data set. Finally, it is ok to simply write a review paper describing a particular topic in phylogenetics in depth. If you choose this route, I will encourage you to write a paper suitable for contribution to Wikipedia (this way, your efforts will survive the course and benefit the broader community). Please get my approval of your chosen topic before doing extensive work on your paper.