Difference between revisions of "Schedule"

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(Opening Reception: 7 PM Sunday, July 17th, Meigs Room, 2nd Floor of Swope)
(Optional programming module:)
 
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== First Week ==
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 +
===[[How to prepare for the Workshop on Molecular Evolution]]===
 
===Please download and install the software listed here: [https://molevol.mbl.edu/index.php/Computer_lab_introduction#Downloads Downloads]===
 
===Please download and install the software listed here: [https://molevol.mbl.edu/index.php/Computer_lab_introduction#Downloads Downloads]===
===Make T shirt suggestions [[Shirts2016]] !===
 
  
Shirts from previous years [https://molevol.mbl.edu/index.php/Previous_MBL_Molecular_Evolution_Workshop_T-Shirts here]!
+
===2019 Dates for the workshop:  1 August to 11 August ===
 +
 
 +
===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]] ===
 +
 
 +
===All teaching sessions will be in room G70 of the [[:file:Loeb.jpeg|Loeb building]] ===
 +
 
 +
<br>
 +
 
 +
=='''Optional programming module:'''==
 +
'''Time:  daily from 8am-8:45am''' <br>
 +
'''Location:  room 263 [[:file:Loeb.jpeg|Loeb building]] (2nd floor)'''<br>
 +
'''Instructor:  [[John Huelsenbeck|Huelsenbeck]]'''<br>
 +
[[File:Programming.pdf]]
 +
 
 +
See also the [[optional programming module]] page.
  
===All morning sessions are in Rowe, afternoons and evenings will be in room G70 of the Loeb building ===
+
Unless otherwise noted, all sessions are in Loeb G70 (basement of Loeb building)
===Opening Reception: 7 PM Sunday, July 17th, Meigs Room, 2nd Floor of Swope===
+
 
{| border="1" width="100%"
+
{| border="0" width="75%"
|- style="background:teal"
+
|-
| align="center" width="14.3%" |  
+
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Thursday, August 1'''
| align="center" width="14.3%" style="color:white" | '''Monday'''<br/>(18 July)
+
|-
| align="center" width="14.3%" style="color:white" | '''Tuesday'''<br/>(19 July)
+
| align="left" width="20%" | '''17:00 - 22:00'''
| align="center" width="14.3%" style="color:white" | '''Wednesday'''<br/>(20 July)
+
| align="left" colspan="2" | Welcome & opening reception Meigs Room in [https://molevol.mbl.edu/index.php/File:Swope_terrace.jpg Swope]
| align="center" width="14.3%" style="color:white" | '''Thursday'''<br/>(21 July)
+
|-
| align="center" width="14.3%" style="color:white" | '''Friday'''<br/>(22 July)
+
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Friday, August 2'''
| align="center" width="14.3%" style="color:white" | '''Saturday'''<br/>(23 July)
+
|-
 +
| 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%" | 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%" | Intro to likelihood
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[John Huelsenbeck|Huelsenbeck]]
 +
| align="left" width="60%" | 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%" | Intro computer lab
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[MarkHolder|Holder]] and TAs
 +
| align="left" width="60%" | 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%" | Intro to maximum likelihood (continued)
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[David Swofford|Swofford]]
 +
| align="left" width="60%" | Model selection
 +
|-
 +
| 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%" | Phylogenomics
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[David Swofford|Swofford]]
 +
| align="left" width="60%" | Model-selection tutorial, PAUP
 +
|-
 +
| 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%" | IQ-TREE
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[Bui Quang Minh|Bui Quang Minh]]
 +
| align="left" width="60%" | IQ-TREE
 +
|-
 +
| 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%" | Bayesian phylogenetics
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Paul Lewis|Lewis]]
 +
| align="left" width="60%" | 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%" | Graphical models
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Michael Landis|Landis]]
 +
| align="left" width="60%" | RevBayes
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
 +
|-
 +
| align="left" width="20%" | '''19:00 - 20:30'''
 +
| align="left" width="20%" | [[Tracy Heath|Heath]]
 +
| align="left" width="60%" | Divergence time estimation
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[Tracy Heath|Heath]]
 +
| align="left" width="60%" | Divergence time estimation Lab
 +
|-
 +
| 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%" | Introduction to The Coalescent
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Laura Kubatko|Kubatko]]
 +
| align="left" width="60%" | Species Tree Estimation
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
 +
|-
 +
| align="left" width="20%" | '''14:00 - 15:30'''
 +
| align="left" width="20%" | [[Solis-Lemus|Solís-Lemus]]
 +
| align="left" width="60%" | Network models
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Solis-Lemus|Solís-Lemus]]
 +
| align="left" width="60%" | Network models
 +
|-
 +
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
 +
|-
 +
| align="left" width="20%" | '''19:00 - 20:30'''
 +
| 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%" | [[Michael Landis|Landis]]/[[Tracy Heath|Heath]]
 +
| align="left" width="60%" | More RevBayes
 +
|-
 +
| 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%" | Substitution models for proteins
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Laura Eme|Laura Eme]]
 +
| align="left" width="60%" | 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%" | 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%" | 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%" | Species Tree Lab I
 +
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | [[Peter Beerli|Beerli]]
 +
| align="left" width="60%" | 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%" | Multilocus phylogeography and phylogenetics
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Scott Edwards|Edwards]]
 +
| align="left" width="60%" | Multilocus phylogeography and phylogenetics
 +
|-
 +
| 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%" | Migrate tutorial
 +
|-
 +
| align="left" width="20%" | '''20:30 - 22:00'''
 +
| align="left" width="20%" | [[Peter Beerli|Beerli]]
 +
| align="left" width="60%" | Migrate tutorial
 
|-
 
|-
| align="center" width="14.3%" height="30" | 09:00-10:30
+
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Friday, August 9'''
| align="center" width="14.3%" | '''[[David Hillis|Hillis]]'''<br/>[http://www.doublehelixranch.com/WoodsHoleMole2016.pdf Introduction]
 
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>([https://molevol.mbl.edu/images/8/86/Lewis_Likelihood_July2015.pdf Likelihood in Phylogenetics])
 
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>([http://phylo.bio.ku.edu/woodshole/Bayesian-WoodsHole_22July2015.pdf Bayesian intro])
 
| align="center" width="14.3%" | '''[[Bielawski|Bielawski]]'''<br/>([http://myweb.dal.ca/js551958/PAML_lab/WH2016_lecture_Parts1and2_FullPage.pdf Codon models, Parts1and2]) 
 
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''<br/>(Phylogenomics: Methods and applications)
 
| align="center" width="14.3%" | '''[[Emily Jane McTavish|McTavish]]'''<br/> (Ascertainment Bias in Phylogenetics)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 10:30-12:00
+
| align="left" width="20%" | '''09:00 - 10:30'''
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''<br/>([http://fasta.bioch.virginia.edu/mol_evol/mol_evol_16.pdf Sequence databases])
+
| align="left" width="20%" | [[Bielawski|Bielawski]]
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>(Substitution models)
+
| align="left" width="60%" | Drift, selection & codon models
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''<br/>([http://phylo.bio.ku.edu/woodshole/Bayesian-WoodsHole_22July2015.pdf Bayesian intro])
 
| align="center" width="14.3%" | '''[[Bielawski|Bielawski]]'''<br/>([http://myweb.dal.ca/js551958/PAML_lab/WH2016_lecture_Part3.pdf Codon models, Part3]) 
 
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''<br/>(Phylogenomics: Methods and applications)
 
| align="center" width="14.3%" | '''[[David Hillis|Hillis]]'''<br/>(History of Phylogenetics and Molecular Evolution)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 12:00-14:00
+
| align="left" width="20%" | '''10:30 - 12:00'''
| align="center" width="14.3%" colspan="6" style="background:gold" | Lunch break
+
| align="left" width="20%" | [[Bielawski|Bielawski]]
 +
| align="left" width="60%" | Statistical analyses
 
|-
 
|-
| align="center" width="14.3%" height="30" | 14:00-15:30
+
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
| align="center" width="14.3%" | '''[[William_Pearson|Pearson]]'''<br/>([http://fasta.bioch.virginia.edu/mol_evol/ FASTA/BLAST lab])
 
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''<br/>(Model selection)<!--( [https://molevol.mbl.edu/images/c/cd/Swofford_WH2015_modsel.pdf Model selection] )-->
 
| align="center" width="14.3%" |  '''[[John Huelsenbeck|Huelsenbeck]]'''<br/>(Bayesian Phylogenetic Analysis)
 
| align="center" width="14.3%" |  '''[[Bielawski|Bielawski]]'''<br/>([https://molevol.mbl.edu/index.php/PAML_notes Lab notes][http://myweb.dal.ca/js551958/PAML_lab/lab.html JB_lab])
 
| align="center" width="14.3%" |  '''[[Tracy Heath|Heath]]'''<br/>([http://phyloworks.org/workshops/divtime.html Divergence time estimation])
 
| align="center" width="14.3%" | '''[[Course Participants|Course Participants]]'''<br/>(Lightning Talks)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 15:30-17:00
+
| align="left" width="20%" | '''14:00 - 15:30'''
| align="center" width="14.3%" | '''[[Emily Jane McTavish|McTavish]]'''<br/>([[Computer lab introduction | Computer lab]])<br>'''  
+
| align="left" width="20%" | [[Belinda Chang|Chang]]
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''<br/>(PAUP*)<!-- ([https://molevol.mbl.edu/images/7/7f/Swofford_WH2015_paup_demo.pdf PAUP slides] [https://molevol.mbl.edu/index.php/PAUP*_Exercise PAUP* Exercise])-->
+
| align="left" width="60%" | Protein evolution & ancestral reconstruction
| align="center" width="14.3%" | '''[[John Huelsenbeck|Huelsenbeck]]'''<br/>(Bayesian Phylogenetic Analysis)
 
| align="center" width="14.3%" | '''[[Bielawski|Bielawski]]'''<br/>([https://molevol.mbl.edu/index.php/PAML_notes Lab notes][http://myweb.dal.ca/js551958/PAML_lab/lab.html JB_lab])
 
| align="center" width="14.3%" | '''[[Tracy Heath|Heath]]'''<br/>([http://phyloworks.org/workshops/divtime.html Divergence time estimation])
 
| align="center" width="14.3%" | '''[[Course Participants|Course Participants]]'''<br/>(Lightning Talks)
 
 
|-
 
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Belinda Chang|Chang]]
 +
| align="left" width="60%" | Adaptive protein evolution
 
|-
 
|-
| align="center" width="14.3%" height="30" | 17:00-19:00
+
| align="left" colspan="3" style="background:#E5E7EC" | Dinner 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%" | '''19:00 - 20:30'''
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''<br/> ([[Multiple Sequence Alignment]])
+
| align="left" width="20%" | [[Bielawski|Bielawski]]
| align="center" width="14.3%" | '''[[Derrick_Zwickl|Zwickl]]'''<br/>([http://phylo.bio.ku.edu/woodshole/Zwickl-WoodsHole2015-lecture.pdf Large scale ML inference])
+
| align="left" width="60%" | PAML lab, lab slides
| align="center" width="14.3%" | '''[[Tracy Heath|Heath]]'''<br/>(Intro to [[RevBayes]])
 
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''<br/>([http://phylo.bio.ku.edu/woodshole/HolderMSALectureWoodsHole2015.pdf Branch support and tests])
 
| align="center" width="14.3%" | <br/>(Participant analyses and discussion with workshop faculty)<br/>
 
| align="center" width="14.3%" |Course dinner/party<br/>Lobster Boil; starts at 5 PM
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 20:30-22:00
+
| align="left" width="20%" | '''20:30 - 22:00'''
| align="center" width="14.3%" | '''[[Emily Jane McTavish|McTavish]]'''<br/>([[Alignment_tutorial | Multiple Sequence Alignment Lab]])
+
| align="left" width="20%" | [[Bielawski|Bielawski]]
| align="center" width="14.3%" | '''[[Derrick_Zwickl|Zwickl]]'''<br/>([http://phylo.bio.ku.edu/slides/GarliDemo/garliExercise.WH2016.html GARLI lab]) 
+
| align="left" width="60%" | Additional resources, advanced lab
| align="center" width="14.3%" | '''[[Michael Landis|Landis]]'''<br/>([[RevBayes]])
 
| align="center" width="14.3%" |  '''[[MarkHolder|Holder]]'''<br/>(Topology testing. continued)
 
| align="center" width="14.3%" |  <br/>(Participant analyses and discussion with workshop faculty)<br/>
 
| align="center" width="14.3%" |  Course dinner/party<br/>Lobster Boil
 
 
|-
 
|-
|}
+
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Saturday, August 10'''
<br/>
+
|-
<!--  
+
| align="left" width="20%" | '''09:00 - 10:30'''
################ Second Week #################
+
| align="left" width="20%" | [[Emilia Huerta-Sanchez|Huerta-Sanchez]]
-->
+
| align="left" width="60%" | Coalescent+selection.
 
+
|-
== Second Week ==
+
| align="left" width="20%" | '''10:30 - 12:00'''
 
+
| align="left" width="20%" | [[Emilia Huerta-Sanchez|Huerta-Sanchez]]
{| border="1" width="57%"
+
| align="left" width="60%" | Coalescent+selection.
|- style="background:teal"
+
|-
| align="center" width="14.3%" |  
+
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
| align="center" width="14.3%" style="color:white" | '''Monday'''<br/>(25 July)
+
|-
| align="center" width="14.3%" style="color:white" | '''Tuesday'''<br/>(26 July)
+
| align="left" width="20%" | '''14:00 - 15:30'''
| align="center" width="14.3%" style="color:white" | '''Wednesday'''<br/>(27 July)
+
| align="left" width="20%" | [[Emily Jane McTavish|McTavish]]
 +
| align="left" width="60%" | gene-tree updating
 +
|-
 +
| align="left" width="20%" | '''15:30 - 17:00'''
 +
| align="left" width="20%" | [[Emily Jane McTavish|McTavish]]
 +
| align="left" width="60%" | gene-tree updating
 +
|-
 +
| 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%" | '''[[Peter Beerli|Beerli]]'''<br/>(Introduction to the coalescent )
+
| 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%" | '''[[Laura Kubatko|Kubatko]]'''<br/>(Phylogenetic networks)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" | 10:30-12:00
+
| align="left" width="20%" | '''20:30 - 22:00'''
| align="center" width="14.3%" | '''[[Laura Kubatko|Kubatko]]'''<br/>(Species Tree Estimation)
+
| 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%" | <br/>(Participant analyses and discussion with workshop faculty)<br/>
 
 
|-
 
|-
| 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%" | '''[[Laura Kubatko|Kubatko]]'''/'''[[David Swofford|Swofford]]''' <br/>(Species Tree Lab I)<br/>
+
| align="left" width="20%" | [[Mark Holder|Holder]]
| align="center" width="14.3%" | '''[[Anne Yoder|Yoder]]''' <br/>(Applications, species delimitation)<br/>
+
| align="left" width="60%" | Scientific ethics, tree testing, Open Tree of Life
| 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%" | '''[[Peter Beerli|Beerli]]'''<br/>(Extensions to coalescence)
+
| align="left" width="20%" | Workshop Faculty
| align="center" width="14.3%" | '''[[Anne Yoder|Yoder]]''' <br/>(Applications, species delimitation)<br/>
+
| 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)<br/>
+
| align="left" width="20%" | Open lab
| align="center" width="14.3%" | '''[[Scott Edwards|Edwards]]''' <br/>([https://molevol.mbl.edu/index.php/Edwards_lab_notes Species Tree Lab II])<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) <br/>
+
| align="left" width="20%" | Open lab
| align="center" width="14.3%" | <br/>(Participant analyses and discussion with workshop faculty)<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 18:12, 23 January 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

Opening Activities: 6 PM Thursday, August 1, Reception in the Meigs Room in the Swope Building

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


Optional programming module:

Time: daily from 8am-8:45am
Location: room 263 Loeb building (2nd floor)
Instructor: Huelsenbeck
File:Programming.pdf

See also the optional programming module page.

Unless otherwise noted, all sessions are in Loeb G70 (basement of Loeb building)

Thursday, August 1
17:00 - 22:00 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 Intro to maximum likelihood (continued)
10:30 - 12:00 Swofford Model selection
Lunch Break
14:00 - 15:30 McTavish Phylogenomics
15:30 - 17:00 Swofford Model-selection tutorial, PAUP
Dinner Break
19:00 - 20:30 Bui Quang Minh IQ-TREE
20:30 - 22:00 Bui Quang Minh IQ-TREE
Sunday, August 4
09:00 - 10:30 Lewis Bayesian phylogenetics
10:30 - 12:00 Lewis Bayesian phylogenetics
Lunch Break
14:00 - 15:30 Landis Graphical models
15:30 - 17:00 Landis RevBayes
Dinner Break
19:00 - 20:30 Heath Divergence time estimation
20:30 - 22:00 Heath Divergence time estimation Lab
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
15:30 - 17:00 Solís-Lemus Network models
Dinner Break
19:00 - 20:30 Huelsenbeck Why I like ML & Bayes
20:30 - 22:00 Landis/Heath More RevBayes
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
15:30 - 17:00 Edwards Multilocus phylogeography and phylogenetics
Dinner Break
19:00 - 20:30 Beerli Migrate tutorial
20:30 - 22:00 Beerli Migrate tutorial
Friday, August 9
09:00 - 10:30 Bielawski Drift, selection & codon models
10:30 - 12:00 Bielawski Statistical analyses
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, lab slides
20:30 - 22:00 Bielawski Additional resources, advanced lab
Saturday, August 10
09:00 - 10:30 Huerta-Sanchez Coalescent+selection.
10:30 - 12:00 Huerta-Sanchez Coalescent+selection.
Lunch Break
14:00 - 15:30 McTavish gene-tree updating
15:30 - 17:00 McTavish gene-tree updating
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, tree testing, Open Tree of Life
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).