Difference between revisions of "Schedule"

From MolEvol
(Make T shirt suggestions Shirts !)
 
(448 intermediate revisions by 26 users not shown)
Line 1: Line 1:
== First Week ==
+
<span style="font-size:large;background-color:yellow;color:red;font-weight:bold">This is the OLD website: the NEW web site is at [https://molevolworkshop.github.io/ molevolworkshop.github.io]. Please go there for information about the 2020 Workshop.</span>
===Make T shirt suggestions [[Shirts2012]] !===
 
  
===All morning sessions are in Rowe, afternoons will be in room G70 of the Loeb building ===
+
===[[How to prepare for the Workshop on Molecular Evolution]]===
{| border="1" width="100%"
+
===Please download and install the software listed here: [https://molevol.mbl.edu/index.php/Computer_lab_introduction#Downloads Downloads]===
|- style="background:teal"
+
 
| align="center" width="14.3%" |  
+
===2019 Dates for the workshop:  1 August to 11 August ===
| align="center" width="14.3%" style="color:white" | '''Monday'''<br/>(23 July)
+
 
| align="center" width="14.3%" style="color:white" | '''Tuesday'''<br/>(24 July)
+
<!-- ===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" | '''Wednesday'''<br/>(25 July)
+
-->
| align="center" width="14.3%" style="color:white" | '''Thursday'''<br/>(26 July)
+
 
| align="center" width="14.3%" style="color:white" | '''Friday'''<br/>(27 July)
+
===All teaching sessions will be in room G70 of the [[:file:Loeb.jpeg|Loeb building]] ===
| align="center" width="14.3%" style="color:white" | '''Saturday'''<br/>(28 July)
+
 
 +
===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="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[MarkHolder|Holder]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/d/dd/Holder_phylo_intro_and_msa.pdf Introduction to phylogenetics]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
 +
|-
 +
| align="left" width="20%" | '''14:00 - 15:30'''
 +
| 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="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[John Huelsenbeck|Huelsenbeck]]
 +
| align="left" width="60%" | [https://molevol.mbl.edu/images/1/1a/WoodsHole2012_1.pdf Likelihood/Simulation]
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
 +
|-
 +
| align="left" width="20%" | '''19:00 - 20:30'''
 +
| align="left" width="20%" | TAs
 +
| align="left" width="60%" | [[Computer lab introduction|Intro computer lab]]
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[MarkHolder|Holder]] and TAs
 +
| align="left" width="60%" | [[Alignment tutorial|Alignment lab]]
 +
|-
 +
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Saturday, August 3'''
 +
|-
 +
| 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-likelihood-part2.pdf Maximum likelihood (continued) and Model selection]
 +
|-
 +
| 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/models.pdf Multiple sequence alignment and intro]
 +
|-
 +
| 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/4/4a/Genomics_WH2019.pdf Phylogenomics]
 +
|-
 +
| 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="center" width="14.3%" height="30" | 09:00-10:30
+
| align="left" width="20%" | '''19:00 - 20:30'''
| align="center" width="14.3%" | '''[[David Hillis|Hillis]]'''<br/>(Intro)
+
| align="left" width="20%" | [[Peter Beerli|Beerli]]
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>(Substitution models)
+
| align="left" width="60%" | [http://peterbeerli.com/workshops/mbl/2018/tutorial/ Population model extimation using MIGRATE ]
| 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" width="20%" | '''20:30 - 22:00'''
| 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="left" width="20%" | [[Peter Beerli|Beerli]]
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>(Likelihoods of trees)
+
| align="left" width="60%" | [http://peterbeerli.com/workshops/mbl/2018/tutorial/ Population model selection using MIGRATE]
| 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
+
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Friday, August 9'''
| 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%" | '''[[William_Pearson|Pearson]]'''<br/>(Sequence databases)
+
| align="left" width="20%" | [[Bielawski|Bielawski]]
| 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%" | [http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/slides/WH2019_Parts1and2_handouts.pdf Drift, selection & codon models (PDF file 1)]
| 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/>([[Media:Meehan_HIV_MBL.zip|Evolution of HIV]])
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 15:30-17:00
+
| align="left" width="20%" | '''10:30 - 12:00'''
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''<br/>(Sequence databases)
+
| align="left" width="20%" | [[Bielawski|Bielawski]]
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''<br/>([[PAUP*_Exercise|PAUP*]])
+
| 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="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/>([[Media:Meehan_Microbiome_MBL.zip|Microbiome Evolution]])
 
 
|-
 
|-
| 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%" | '''[[William_Pearson|Pearson]]'''<br/>([http://fasta.bioch.virginia.edu/mol_evol/ FASTA/BLAST lab])
+
| align="left" width="20%" | [[Belinda Chang|Chang]]
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''<br/>([http://phylo.bio.ku.edu/woodshole/HolderTestingLectureWoodsHole2012.pdf Topology testing]])
+
| align="left" width="60%" | [https://molevol.mbl.edu/images/3/33/Protein_Evolution_%26_Ancestral_Reconstruction.pdf Protein evolution & ancestral reconstruction]
| 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_lab])
 
| align="center" width="14.3%" | '''[[Tracy Heath|Heath]]'''<br/>(Divergence time estimation)
 
| align="center" width="14.3%" | Course dinner/party<br/>Lobster Broil; starts at 6 PM
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 20:30-22:00
+
| align="left" width="20%" | '''15:30 - 17:00'''
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''<br/>([http://fasta.bioch.virginia.edu/mol_evol/ FASTA/BLAST lab])
+
| align="left" width="20%" | [[Belinda Chang|Chang]]
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''<br/>([[ParametricBootstrappingLab|Branch support and tests]])
+
| align="left" width="60%" | [https://molevol.mbl.edu/images/a/a3/Adaptive_Protein_Evolution.pdf Adaptive protein evolution]
| 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_lab])
 
| align="center" width="14.3%" |  '''[[Tracy Heath|Heath]]'''<br/>(BEAST)
 
| align="center" width="14.3%" |  Course dinner/party<br/>Lobster Broil
 
 
|-
 
|-
|}
+
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
<br/>
+
|-
<!--  
+
| align="left" width="20%" | '''19:00 - 20:30'''
################ Second Week #################
+
| 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]
 
+
|-
== Second Week ==
+
| align="left" width="20%" | '''20:30 - 22:00'''
 
+
| align="left" width="20%" | [[Bielawski|Bielawski]]
{| border="1" width="57%"
+
| 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]
|- style="background:teal"
+
|-
| align="center" width="14.3%" |  
+
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Saturday, August 10'''
| align="center" width="14.3%" style="color:white" | '''Monday'''<br/>(30 July)
+
|-
| align="center" width="14.3%" style="color:white" | '''Tuesday'''<br/>(31 July)
+
| align="left" width="20%" | '''09:00 - 10:30'''
| align="center" width="14.3%" style="color:white" | '''Wednesday'''<br/>(1 August)
+
| 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 15:47, 9 December 2019

This is the OLD website: the NEW web site is at molevolworkshop.github.io. Please go there for information about the 2020 Workshop.

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).