Difference between revisions of "Schedule"

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(All morning sessions are in Rowe, afternoons will be in room G70 of the Loeb building)
(Optional programming module:)
 
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== First Week ==
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===Sunday, 22 July 2012: Arrival and '''opening reception''' in the Meigs Room, Swope Building 7pm - 9pm===
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===[[How to prepare for the Workshop on Molecular Evolution]]===
===All morning sessions are in Rowe, afternoons will be in room G70 of the Loeb building ===
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===Please download and install the software listed here: [https://molevol.mbl.edu/index.php/Computer_lab_introduction#Downloads Downloads]===
{| border="1" width="100%"
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|- style="background:teal"
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===2019 Dates for the workshop:  1 August to 11 August ===
| align="center" width="14.3%" |  
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| align="center" width="14.3%" style="color:white" | '''Monday'''<br/>(23 July)
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<!-- ===Opening Activities: <span style="color:red">6 PM Thursday, August 1</span>, Reception in the Meigs Room in the [[:file:Swope-with-Eel-pond.jpg|Swope Building]] ===
| align="center" width="14.3%" style="color:white" | '''Tuesday'''<br/>(24 July)
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-->
| align="center" width="14.3%" style="color:white" | '''Wednesday'''<br/>(25 July)
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| align="center" width="14.3%" style="color:white" | '''Thursday'''<br/>(26 July)
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===All teaching sessions will be in room G70 of the [[:file:Loeb.jpeg|Loeb building]] ===
| align="center" width="14.3%" style="color:white" | '''Friday'''<br/>(27 July)
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| align="center" width="14.3%" style="color:white" | '''Saturday'''<br/>(28 July)
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===2019 Student Presentations [https://molevol.mbl.edu/images/3/33/MOLE2019.1.pdf Part1] [https://molevol.mbl.edu/images/4/42/MOLE2019.2.pdf Part2]===
 +
 
 +
===[https://molevol.mbl.edu/index.php/Shirts2019 2019 T-Shirt contest]===
 +
 
 +
<br>
 +
 
 +
=='''Optional programming module:'''==
 +
<!--
 +
Starting Saturday 3 Aug. <br>
 +
'''Time:  daily from 8am-8:45am''' <br>
 +
'''Location:  room G70 [[:file:Loeb.jpeg|Loeb building]]'''<br>
 +
'''Instructor:  [[John Huelsenbeck|Huelsenbeck]]'''<br>
 +
[[File:Programming.pdf]]
 +
-->
 +
See the [[optional programming module]] page for info on John Huelsenbeck's 8:00AM programming tutorials
 +
 
 +
All sessions are in '''Loeb G70''' (basement of Loeb building)
 +
 
 +
{| border="0" width="75%"
 +
|-
 +
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Thursday, August 1'''
 +
|-
 +
| align="left" width="20%" | '''18:00 - 21:00'''
 +
| align="left" colspan="2" | Welcome & opening reception Meigs Room in [https://molevol.mbl.edu/index.php/File:Swope_terrace.jpg Swope]
 +
|-
 +
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Friday, August 2'''
 +
|-
 +
| align="left" width="20%" | '''09:00 - 10:30'''
 +
| align="left" width="20%" | [[MarkHolder|Holder]]
 +
| align="left" width="60%" | Welcome & 1 min Student Presentations
 
|-
 
|-
| align="center" width="14.3%" height="30" | 09:00-10:30
+
| align="left" width="20%" | '''10:30 - 12:00'''
| align="center" width="14.3%" | '''[[David Hillis|Hillis]]'''<br/>(Intro)
+
| align="left" width="20%" | [[MarkHolder|Holder]]
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>(Substitution models)
+
| align="left" width="60%" | [https://molevol.mbl.edu/images/d/dd/Holder_phylo_intro_and_msa.pdf Introduction to phylogenetics]
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>(Bayesian intro)
 
| align="center" width="14.3%" | '''[[Bielawski|Bielawski]]'''<br/>(Codon models) 
 
| align="center" width="14.3%" |  '''[[Peter Beerli|Beerli]]'''<br/>(Coalescence)
 
| align="center" width="14.3%" | '''[[User:Felsenst|Felsenstein]]'''<br/>(Phylogenetics of quantitative characters)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 10:30-12:00
+
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
| align="center" width="14.3%" | '''TAs'''<br/>([[Computer lab introduction|Computer lab intro]])<br>'''[[MarkHolder|Holder]]'''<br/> ([http://phylo.bio.ku.edu/woodshole/HolderMSALectureWoodsHole2012.pdf Alignment]) <br/>  [[MSA_lab|Alignment Lab]]
 
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>(Likelihoods of trees)
 
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>(Bayesian intro)
 
| align="center" width="14.3%" | '''[[Bielawski|Bielawski]]'''<br/>(Codon models) 
 
| align="center" width="14.3%" | '''[[Peter Beerli|Beerli]]'''<br/>(Coalescence)
 
| align="center" width="14.3%" | '''[[User:Felsenst|Felsenstein]]'''<br/>(Historical Perspective of Phylogenetics)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 12:00-14:00
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| align="left" width="20%" | '''14:00 - 15:30'''
| align="center" width="14.3%" colspan="6" style="background:gold" | Lunch break
+
| align="left" width="20%" | [[Paul Lewis|Lewis]]
 +
| align="left" width="60%" | [http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/wh2019/lewis-likelihood-part1.pdf Intro to likelihood]
 
|-
 
|-
| align="center" width="14.3%" height="30" | 14:00-15:30
+
| align="left" width="20%" | '''15:30 - 17:00'''
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''<br/>(Sequence databases)
+
| align="left" width="20%" | [[John Huelsenbeck|Huelsenbeck]]
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''<br/>([http://phylo.bio.ku.edu/woodshole/swofford_WH2011_modsel.pdf Model selection])
+
| align="left" width="60%" | [https://molevol.mbl.edu/images/1/1a/WoodsHole2012_1.pdf Likelihood/Simulation]
| align="center" width="14.3%" | '''[[John Huelsenbeck|Huelsenbeck]]'''<br/>(Bayesian Phylogenetic Analysis: [[Media:WoodsHole2012_1.pdf|I]], [[Media:WoodsHole2012_2.pdf|II]], [[Media:WoodsHoleHandout.pdf|Supp.]] [http://phylo.bio.ku.edu/woodshole/simwithdice.nex simwithdice.nex])
 
| align="center" width="14.3%" | '''[[Derrick_Zwickl|Zwickl]]'''<br/>(Large scale ML inference) 
 
| align="center" width="14.3%" |  '''[[Laura Kubatko|Kubatko]]'''<br/>(Species Tree Estimation)
 
| align="center" width="14.3%" | '''[[Conor Meehan|Meehan]]'''<br/>(Evolution of HIV)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 15:30-17:00
+
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''<br/>(Sequence databases)
 
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''<br/>([[PAUP*_Exercise|PAUP*]])
 
| align="center" width="14.3%" |  '''[[John Huelsenbeck|Huelsenbeck]]'''<br/>(Bayesian Phylogenetic Analysis: [[Media:WoodsHole2012_1.pdf|I]], [[Media:WoodsHole2012_2.pdf|II]], [[Media:WoodsHoleHandout.pdf|Supp.]])
 
| align="center" width="14.3%" | '''[[Derrick_Zwickl|Zwickl]]'''<br/>([http://phylo.bio.ku.edu/slides/GarliDemo/garliExercise.html GARLI lab]) 
 
| align="center" width="14.3%" |  '''[[Laura Kubatko|Kubatko]]'''<br/>(Species Tree Estimation)
 
| align="center" width="14.3%" |  '''[[Conor Meehan|Meehan]]'''<br/>(Microbiome Evolution)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 17:00-19:00
+
| align="left" width="20%" | '''19:00 - 20:30'''
| align="center" width="14.3%" colspan="6" style="background:gold" | Dinner break
+
| align="left" width="20%" | TAs
 +
| align="left" width="60%" | [[Computer lab introduction|Intro computer lab]]
 
|-
 
|-
| align="center" width="14.3%" height="30" | 19:00-20:30
+
| align="left" width="20%" | '''20:30 - 22:00'''
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''<br/>([http://fasta.bioch.virginia.edu/mol_evol/ FASTA/BLAST lab])
+
| align="left" width="20%" | [[MarkHolder|Holder]] and TAs
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''<br/>([http://phylo.bio.ku.edu/woodshole/HolderTestingLectureWoodsHole2012.pdf Topology testing]])
+
| align="left" width="60%" | [[Alignment tutorial|Alignment lab]]
| align="center" width="14.3%" | '''[[John Huelsenbeck|Huelsenbeck]]'''<br/>[https://molevol.mbl.edu/wiki/index.php/MrBayes MrBayes]
 
| align="center" width="14.3%" | '''[[Bielawski|Bielawski]]'''<br/>('''[[PAML | PAML]]''')
 
| align="center" width="14.3%" | '''[[Tracy Heath|Heath]]'''<br/>(Divergence time estimation)
 
| align="center" width="14.3%" | Course dinner/party<br/>Lobster Broil
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 20:30-22:00
+
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Saturday, August 3'''
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''<br/>([http://fasta.bioch.virginia.edu/mol_evol/ FASTA/BLAST lab])
 
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''<br/>([[ParametricBootstrappingLab|Branch support and tests]])
 
| align="center" width="14.3%" |  '''[[John Huelsenbeck|Huelsenbeck]]'''<br/>[https://molevol.mbl.edu/wiki/index.php/MrBayes MrBayes]
 
| align="center" width="14.3%" | '''[[Bielawski|Bielawski]]'''<br/>('''[[PAML | PAML]]''' [http://myweb.dal.ca/js551958/PAML_lab/lab.html JB])
 
| align="center" width="14.3%" |  '''[[Tracy Heath|Heath]]'''<br/>(BEAST)
 
| align="center" width="14.3%" |  Course dinner/party<br/>Lobster Broil
 
 
|-
 
|-
|}
+
| align="left" width="20%" | '''09:00 - 10:30'''
<br/>
+
| align="left" width="20%" | [[Paul Lewis|Lewis]]
<!--  
+
| align="left" width="60%" | [http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/wh2019/lewis-likelihood-part2.pdf Maximum likelihood (continued) and Model selection]
################ Second Week #################
+
|-
-->
+
| align="left" width="20%" | '''10:30 - 12:00'''
 
+
| align="left" width="20%" | [[Paul Lewis|Lewis]]
== Second Week ==
+
| align="left" width="60%" | [http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/wh2019/models.pdf Multiple sequence alignment and intro]
 
+
|-
{| border="1" width="57%"
+
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
|- style="background:teal"
+
|-
| align="center" width="14.3%" |  
+
| align="left" width="20%" | '''14:00 - 15:30'''
| align="center" width="14.3%" style="color:white" | '''Monday'''<br/>(30 July)
+
| align="left" width="20%" | [[Emily Jane McTavish|McTavish]]
| align="center" width="14.3%" style="color:white" | '''Tuesday'''<br/>(31 July)
+
| align="left" width="60%" | [https://molevol.mbl.edu/images/4/4a/Genomics_WH2019.pdf Phylogenomics]
| align="center" width="14.3%" style="color:white" | '''Wednesday'''<br/>(1 August)
+
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[MarkHolder|Holder]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/8/83/Tree-searching-mth-2019.pdf Tree searching]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
 +
|-
 +
| align="left" width="20%" | '''19:00 - 20:30'''
 +
| align="left" width="20%" | [[Bui Quang Minh|Bui Quang Minh]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/c/c8/Minh-2019-lecture-material.pdf IQ-TREE Introduction]
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[Bui Quang Minh|Bui Quang Minh]]
 +
| align="left" width="60%" | [http://www.iqtree.org/workshop/molevol2019 IQ-TREE Tutorial], [https://molevol.mbl.edu/images/7/75/Minh_2019_Tutorial-solutions.pdf Tutorial solutions]
 +
|-
 +
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Sunday, August 4'''
 +
|-
 +
| align="left" width="20%" | '''09:00 - 10:30'''
 +
| align="left" width="20%" | [[Paul Lewis|Lewis]]
 +
| align="left" width="60%" | [http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/wh2019/lewis-bayesian-part1.pdf Bayesian phylogenetics]
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Paul Lewis|Lewis]]
 +
| align="left" width="60%" | [http://hydrodictyon.eeb.uconn.edu/people/plewis/downloads/wh2019/lewis-bayesian-part2.pdf Bayesian phylogenetics]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
 +
|-
 +
| align="left" width="20%" | '''14:00 - 15:30'''
 +
| align="left" width="20%" | [[Michael Landis|Landis]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/4/44/Lecture_phylo_pgm_mlandis_WH2019.pdf Phylogenetics & graphical models]
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Tracy Heath|Heath]]
 +
| align="left" width="60%" | [https://figshare.com/articles/Bayesian_Divergence-Time_Estimation_Lecture/6849005 Divergence time estimation] continued
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
 +
|-
 +
| align="left" width="20%" | '''19:00 - 20:00'''
 +
| align="left" width="20%" | [[Tracy Heath|Heath]]
 +
| align="left" width="60%" | [https://figshare.com/articles/Bayesian_Divergence-Time_Estimation_Lecture/6849005 Divergence time estimation] continued
 +
|-
 +
| align="left" width="20%" | '''20:00 - 20:30'''
 +
| align="left" width="20%" | [[Michael Landis|Landis]]
 +
| align="left" width="60%" | [https://revbayes.github.io/tutorials/intro/ Intro to RevBayes]
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[Michael Landis|Landis]]
 +
| align="left" width="60%" | [https://revbayes.github.io/tutorials/ctmc/ Gene tree estimation with RevBayes]
 +
|-
 +
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Monday, August 5'''
 +
|-
 +
| align="left" width="20%" | '''09:00 - 10:30'''
 +
| align="left" width="20%" | [[Peter Beerli|Beerli]]
 +
| align="left" width="60%" | [https://peterbeerli.com/workshops/mbl/2019/talk1.pdf Introduction to The Coalescent]
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Laura Kubatko|Kubatko]]
 +
| align="left" width="60%" | [https://www.asc.ohio-state.edu/kubatko.2//SpeciesTreeEstimation2019.pdf Species Tree Estimation]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
 +
|-
 +
| align="left" width="20%" | '''14:00 - 15:30'''
 +
| align="left" width="20%" | [[Claudia Solis-Lemus|Solís-Lemus]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/0/07/Talk-networks-mbl.pdf Network models lecture]
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Claudia Solis-Lemus|Solís-Lemus]]
 +
| align="left" width="60%" | [https://github.com/crsl4/PhyloNetworks.jl/wiki Network models tutorial]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
 +
|-
 +
| align="left" width="20%" | '''19:00 - 20:30'''
 +
| align="left" width="20%" | [[David Swofford|Swofford]]
 +
| align="left" width="60%" | [[David Swofford|Intro to PAUP*]]
 +
|-
 +
| align="left" width="20%" |
 +
| align="left" width="20%" | [[John Huelsenbeck|Huelsenbeck]]
 +
| align="left" width="60%" | Why I like ML & Bayes
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[Will Pett|Pett]]
 +
| align="left" width="60%" | [https://revbayes.github.io/tutorials/fbd/fbd_specimen.html Divergence time estimation Lab]
 +
|-
 +
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Tuesday, August 6'''
 +
|-
 +
| align="left" width="20%" | '''09:00 - 10:30'''
 +
| align="left" width="20%" | [[Laura Eme|Laura Eme]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/b/b0/Phylogenomics_EmeLaura_WoodsHole2019_4.pdf Substitution models for proteins]
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Laura Eme|Laura Eme]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/b/b0/Phylogenomics_EmeLaura_WoodsHole2019_4.pdf#page=72 Multi-gene phylogenetics: methods & applications]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
 +
|-
 +
| align="left" width="20%" | '''14:00 - 15:30'''
 +
| align="left" width="20%" | [[Anne Yoder|Anne Yoder]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/5/56/Yoder_MBL.8.2019.pdf What are we even talking about when we say "species tree"?]
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Anne Yoder|Anne Yoder]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/5/56/Yoder_MBL.8.2019.pdf What are we even talking about when we say "species tree"?]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Break
 +
|-
 +
| align="left" width="20%" | '''19:00 - 22:00'''
 +
| align="left" width="20%" | Course Dinner Party
 +
| align="left" width="60%" | Swope Terrace
 +
|-
 +
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Wednesday, August 7'''
 +
|-
 +
| align="left" width="20%" | '''09:00 - 22:00'''
 +
| align="left" width="20%" | '''Free Day'''
 +
| align="left" width="60%" | On your own: Whale watching, Martha's Vineyard, sleep, ...
 +
|-
 +
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Thursday, August 8'''
 +
|-
 +
| align="left" width="20%" | '''09:00 - 10:30'''
 +
| align="left" width="20%" | [[Laura Kubatko|Kubatko]]/[[David Swofford|Swofford]]
 +
| align="left" width="60%" | [http://phylosolutions.com/tutorials/wh2019-svdq-astral/species-trees-tutorial.html Species Tree Lab I]
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Peter Beerli|Beerli]]
 +
| align="left" width="60%" | [http://peterbeerli.com/workshops/mbl/2018/talk2.pdf Extension of the basic coalescent]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
 +
|-
 +
| align="left" width="20%" | '''14:00 - 15:30'''
 +
| align="left" width="20%" | [[Scott Edwards|Edwards]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/7/79/Edwards_MBL_2019_partI.pdf Multilocus phylogeography and phylogenetics I]
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Scott Edwards|Edwards]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/9/92/Edwards_MBL_2019_partII.pdf Multilocus phylogeography and phylogenetics II]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
 +
|-
 +
| align="left" width="20%" | '''19:00 - 20:30'''
 +
| align="left" width="20%" | [[Peter Beerli|Beerli]]
 +
| align="left" width="60%" | [http://peterbeerli.com/workshops/mbl/2018/tutorial/ Population model extimation using MIGRATE ]
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[Peter Beerli|Beerli]]
 +
| align="left" width="60%" | [http://peterbeerli.com/workshops/mbl/2018/tutorial/ Population model selection using MIGRATE]
 +
|-
 +
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Friday, August 9'''
 +
|-
 +
| align="left" width="20%" | '''09:00 - 10:30'''
 +
| align="left" width="20%" | [[Bielawski|Bielawski]]
 +
| align="left" width="60%" | [http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/slides/WH2019_Parts1and2_handouts.pdf Drift, selection & codon models (PDF file 1)]
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Bielawski|Bielawski]]
 +
| align="left" width="60%" | [http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/slides/WH2019_Parts3and4_handouts.pdf Statistical analysis and testing mechanism (PDF file 2)]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
 +
|-
 +
| align="left" width="20%" | '''14:00 - 15:30'''
 +
| align="left" width="20%" | [[Belinda Chang|Chang]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/3/33/Protein_Evolution_%26_Ancestral_Reconstruction.pdf Protein evolution & ancestral reconstruction]
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Belinda Chang|Chang]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/a/a3/Adaptive_Protein_Evolution.pdf Adaptive protein evolution]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
 +
|-
 +
| align="left" width="20%" | '''19:00 - 20:30'''
 +
| align="left" width="20%" | [[Bielawski|Bielawski]]
 +
| align="left" width="60%" | [http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/lab.html PAML lab website], [http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/slides/pamlDEMO_slides.pdf lab slides]
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[Bielawski|Bielawski]]
 +
| align="left" width="60%" | [http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/Resources.html Additional resources], [https://bitbucket.org/EvoWorks/protocol-inference-of-episodic-selection/downloads advanced lab]
 +
|-
 +
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Saturday, August 10'''
 +
|-
 +
| align="left" width="20%" | '''09:00 - 10:30'''
 +
| align="left" width="20%" | [[Emilia Huerta-Sanchez|Huerta-Sanchez]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/7/73/MBL_WoodsHole_Aug10_2019_Part1.pdf Population genetics + selection I]
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Emilia Huerta-Sanchez|Huerta-Sanchez]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/c/cc/MBL_WoodsHole_Aug10_2019_Part2.pdf Population genetics + selection II]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
 +
|-
 +
| align="left" width="20%" | '''14:00 - 15:30'''
 +
| align="left" width="20%" | [[Emily Jane McTavish|McTavish]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/7/77/Opentree_2019.pdf Open Tree of Life, gene-tree updating Slides]
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Emily Jane McTavish|McTavish]]
 +
| align="left" width="60%" | [https://github.com/snacktavish/Mole2019/blob/master/TreeComparison.md Open Tree of Life, gene-tree updating Lab]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
 
|-
 
|-
| align="center" width="14.3%" height="30" | 09:00-10:30
+
| align="left" width="20%" | '''19:00 - 20:30'''
| align="center" width="14.3%" | '''[[Sara Sawyer|Sawyer]]'''<br/>(Applications of Molecular Evolution to Understanding Disease)
+
| align="left" width="20%" | [[Lacey Knowles|Knowles]]
| align="center" width="14.3%" | '''[[Scott Edwards|Edwards]]'''<br/>(Multilocus phylogeography and phylogenetics)
+
| align="left" width="60%" | Evolutionary applications of genomic data
| align="center" width="14.3%" | '''[[Harold Zakon|Zakon]]'''<br/>(Molecular Evolution of Sodium Channels)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 10:30-12:00
+
| align="left" width="20%" | '''20:30 - 22:00'''
| align="center" width="14.3%" | '''[[Sara Sawyer|Sawyer]]'''<br/>(Applications of Molecular Evolution to Understanding Disease)
+
| align="left" width="20%" | [[Lacey Knowles|Knowles]]
| align="center" width="14.3%" | '''[[Scott Edwards|Edwards]]'''<br/>(Multilocus phylogeography and phylogenetics)
+
| align="left" width="60%" | Evolutionary applications of genomic data
| align="center" width="14.3%" | '''[[Harold Zakon|Zakon]]'''<br/>(Molecular Evolution of Sodium Channels)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 12:00-14:00
+
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Sunday, August 11'''
| align="center" width="14.3%" colspan="6" style="background:gold" | Lunch break
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 14:00-15:30
+
| align="left" width="20%" | '''09:00 - 10:30'''
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''<br/>(Phylogenomics: applications)
+
| align="left" width="20%" | [[Mark Holder|Holder]]
| align="center" width="14.3%" | '''[[Antonis Rokas|Rokas]]'''<br/>(Genome evolution)
+
| align="left" width="60%" | [https://molevol.mbl.edu/images/8/81/Holder_last_lecture_2019.pdf Scientific ethics; frequentist tests of tree topology]
| align="center" width="14.3%" |
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 15:30-17:00
+
| align="left" width="20%" | '''10:30 - 12:00'''
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''<br/>(Phylogenomics: applications)
+
| align="left" width="20%" | Workshop Faculty
| align="center" width="14.3%" | '''[[Antonis Rokas|Rokas]]'''<br/>(Genome evolution)
+
| align="left" width="60%" | Participant Discussions
| align="center" width="14.3%" |  
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 17:00-19:00
+
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
| align="center" width="14.3%" colspan="6" style="background:gold" | Dinner break
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 19:00-20:30
+
| align="left" width="20%" | '''14:00 - 15:30'''
| align="center" width="14.3%" | '''[[Peter Beerli|Beerli]]''' <br/>([[Migrate tutorial]] and [[Lamarc tutorial]])<br/>
+
| align="left" width="20%" | Open lab
| align="center" width="14.3%" | '''[[Laura Kubatko|Kubatko]] and [[Scott Edwards|Edwards]]''' <br/>(Species Tree software)<br/>
+
| align="left" width="60%" |  
| align="center" width="14.3%" |  
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 20:30-22:00
+
| align="left" width="20%" | '''15:30 - 17:00'''
| align="center" width="14.3%" | '''[[Peter Beerli|Beerli]]''' <br/>([[Migrate tutorial]] and [[Lamarc tutorial]]) <br/>
+
| align="left" width="20%" | Open lab
| align="center" width="14.3%" | '''[[Laura Kubatko|Kubatko]] and [[Scott Edwards|Edwards]]''' <br/>(Species Tree software)<br/>
+
| align="left" width="60%" |  
| align="center" width="14.3%" |  
 
 
|-
 
|-
 
|}
 
|}
 +
<br/>
 +
 +
 +
See the [[Schedule_2018|Schedule_2018]] page for last year's schedule (with links to lecture slides from last year).

Latest revision as of 09:17, 11 August 2019

How to prepare for the Workshop on Molecular Evolution

Please download and install the software listed here: Downloads

2019 Dates for the workshop: 1 August to 11 August

All teaching sessions will be in room G70 of the Loeb building

2019 Student Presentations Part1 Part2

2019 T-Shirt contest


Optional programming module:

See the optional programming module page for info on John Huelsenbeck's 8:00AM programming tutorials

All sessions are in Loeb G70 (basement of Loeb building)

Thursday, August 1
18:00 - 21:00 Welcome & opening reception Meigs Room in Swope
Friday, August 2
09:00 - 10:30 Holder Welcome & 1 min Student Presentations
10:30 - 12:00 Holder Introduction to phylogenetics
Lunch Break
14:00 - 15:30 Lewis Intro to likelihood
15:30 - 17:00 Huelsenbeck Likelihood/Simulation
Dinner Break
19:00 - 20:30 TAs Intro computer lab
20:30 - 22:00 Holder and TAs Alignment lab
Saturday, August 3
09:00 - 10:30 Lewis Maximum likelihood (continued) and Model selection
10:30 - 12:00 Lewis Multiple sequence alignment and intro
Lunch Break
14:00 - 15:30 McTavish Phylogenomics
15:30 - 17:00 Holder Tree searching
Dinner Break
19:00 - 20:30 Bui Quang Minh IQ-TREE Introduction
20:30 - 22:00 Bui Quang Minh IQ-TREE Tutorial, Tutorial solutions
Sunday, August 4
09:00 - 10:30 Lewis Bayesian phylogenetics
10:30 - 12:00 Lewis Bayesian phylogenetics
Lunch Break
14:00 - 15:30 Landis Phylogenetics & graphical models
15:30 - 17:00 Heath Divergence time estimation continued
Dinner Break
19:00 - 20:00 Heath Divergence time estimation continued
20:00 - 20:30 Landis Intro to RevBayes
20:30 - 22:00 Landis Gene tree estimation with RevBayes
Monday, August 5
09:00 - 10:30 Beerli Introduction to The Coalescent
10:30 - 12:00 Kubatko Species Tree Estimation
Lunch Break
14:00 - 15:30 Solís-Lemus Network models lecture
15:30 - 17:00 Solís-Lemus Network models tutorial
Dinner Break
19:00 - 20:30 Swofford Intro to PAUP*
Huelsenbeck Why I like ML & Bayes
20:30 - 22:00 Pett Divergence time estimation Lab
Tuesday, August 6
09:00 - 10:30 Laura Eme Substitution models for proteins
10:30 - 12:00 Laura Eme Multi-gene phylogenetics: methods & applications
Lunch Break
14:00 - 15:30 Anne Yoder What are we even talking about when we say "species tree"?
15:30 - 17:00 Anne Yoder What are we even talking about when we say "species tree"?
Break
19:00 - 22:00 Course Dinner Party Swope Terrace
Wednesday, August 7
09:00 - 22:00 Free Day On your own: Whale watching, Martha's Vineyard, sleep, ...
Thursday, August 8
09:00 - 10:30 Kubatko/Swofford Species Tree Lab I
10:30 - 12:00 Beerli Extension of the basic coalescent
Lunch Break
14:00 - 15:30 Edwards Multilocus phylogeography and phylogenetics I
15:30 - 17:00 Edwards Multilocus phylogeography and phylogenetics II
Dinner Break
19:00 - 20:30 Beerli Population model extimation using MIGRATE
20:30 - 22:00 Beerli Population model selection using MIGRATE
Friday, August 9
09:00 - 10:30 Bielawski Drift, selection & codon models (PDF file 1)
10:30 - 12:00 Bielawski Statistical analysis and testing mechanism (PDF file 2)
Lunch Break
14:00 - 15:30 Chang Protein evolution & ancestral reconstruction
15:30 - 17:00 Chang Adaptive protein evolution
Dinner Break
19:00 - 20:30 Bielawski PAML lab website, lab slides
20:30 - 22:00 Bielawski Additional resources, advanced lab
Saturday, August 10
09:00 - 10:30 Huerta-Sanchez Population genetics + selection I
10:30 - 12:00 Huerta-Sanchez Population genetics + selection II
Lunch Break
14:00 - 15:30 McTavish Open Tree of Life, gene-tree updating Slides
15:30 - 17:00 McTavish Open Tree of Life, gene-tree updating Lab
Dinner Break
19:00 - 20:30 Knowles Evolutionary applications of genomic data
20:30 - 22:00 Knowles Evolutionary applications of genomic data
Sunday, August 11
09:00 - 10:30 Holder Scientific ethics; frequentist tests of tree topology
10:30 - 12:00 Workshop Faculty Participant Discussions
Lunch Break
14:00 - 15:30 Open lab
15:30 - 17:00 Open lab



See the Schedule_2018 page for last year's schedule (with links to lecture slides from last year).