Difference between revisions of "Schedule"

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<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>
  
 
===[[How to prepare for the Workshop on Molecular Evolution]]===
 
===[[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]===
  
===Opening Activities: <span style="color:red">6 PM Thursday, July 19th</span>, Reception in the Meigs Room in the [[:file:Swope-with-Eel-pond.jpg|Swope Building]] ===
+
===2019 Dates for the workshop: 1 August to 11 August ===
  
===All morning sessions are in the Speck Auditorium in the [[:file:rowe.jpg|Rowe Building]], afternoons and evenings will be in room G70 of the [[:file:Loeb.jpeg|Loeb building]] ===
+
<!-- ===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]] ===
 +
 
 +
===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]===
  
===Group photo: Ts July 24th, 10:30 (tentative) outside of Rowe building===
 
 
<br>
 
<br>
  
 
=='''Optional programming module:'''==
 
=='''Optional programming module:'''==
 +
<!--
 +
Starting Saturday 3 Aug. <br>
 
'''Time:  daily from 8am-8:45am''' <br>
 
'''Time:  daily from 8am-8:45am''' <br>
'''Location:  room 263 [[:file:Loeb.jpeg|Loeb building]] (2nd floor)'''<br>
+
'''Location:  room G70 [[:file:Loeb.jpeg|Loeb building]]'''<br>
 
'''Instructor:  [[John Huelsenbeck|Huelsenbeck]]'''<br>
 
'''Instructor:  [[John Huelsenbeck|Huelsenbeck]]'''<br>
 
[[File:Programming.pdf]]
 
[[File:Programming.pdf]]
 +
-->
 +
See the [[optional programming module]] page for info on John Huelsenbeck's 8:00AM programming tutorials
  
See also the [[optional programming module]] page.
+
All sessions are in '''Loeb G70''' (basement of Loeb building)
  
== First Week ==
+
{| border="0" width="75%"
 
+
|-
{| border="1" width="65%"
+
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Thursday, August 1'''
|- style="background:SteelBlue"
+
|-
| align="center" width="14.3%" |  
+
| align="left" width="20%" | '''18:00 - 21:00'''
| align="center" width="14.3%" style="color:white" | '''Thursday'''<br/>(19 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" | '''Friday'''<br/>(20 July)
+
|-
| align="center" width="14.3%" style="color:white" | '''Saturday'''<br/>(21 July)
+
| align="center" colspan="3"  style="background:SteelBlue;color:white" | '''Friday, August 2'''
| align="center" width="14.3%" style="color:white" | '''Sunday'''<br/>(22 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%" | [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="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="center" width="14.3%" height="30" style="background:#c8ccd1"  | '''09:00-10:30'''
+
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
| align="center" width="14.3%" style="background:#DCDCDC" |
 
| align="center" width="14.3%" | '''[[Bielawski|Bielawski]]'''      <br/>(Welcome &<br/> '''1 min Student Presentations''')
 
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''      <br/>(ML phylogenetics)
 
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''      <br/>(Bayesian phylogenetics)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" style="background:#c8ccd1"  | '''10:30-12:00'''
+
| align="left" width="20%" | '''19:00 - 20:30'''
| align="center" width="14.3%" style="background:#DCDCDC" |
+
| align="left" width="20%" | [[Bielawski|Bielawski]]
| align="center" width="14.3%" | '''[[MarkHolder|Holder]]'''  <br/>([http://phylo.bio.ku.edu/woodshole/phylogenetics_intro_2018.pdf Intro. to Phylogenetics])
+
| 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="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''      <br/>(ML phylogenetics)
 
| align="center" width="14.3%" | '''[[Paul Lewis|Lewis]]'''      <br/>(Bayesian phylogenetics)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" style="background:#c8ccd1"  | '''12:00-14:00'''
+
| align="left" width="20%" | '''20:30 - 22:00'''
| align="center" width="14.3%" colspan="6" style="background:#DCDCDC" | Lunch break
+
| 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" width="14.3%" height="30" style="background:#c8ccd1"  | '''14:00-15:30'''
+
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Saturday, August 10'''
| align="center" width="14.3%" style="background:#DCDCDC" |
 
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''                <br/>(Phylogenomics & methods)
 
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''        <br/>(Model selection)
 
| align="center" width="14.3%" | '''[[John Huelsenbeck|Huelsenbeck]]'''   <br/>(Simulation lab++)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" style="background:#c8ccd1"  | '''15:30-17:00'''
+
| align="left" width="20%" | '''09:00 - 10:30'''
| align="center" width="14.3%" style="background:#DCDCDC" |
+
| align="left" width="20%" | [[Emilia Huerta-Sanchez|Huerta-Sanchez]]
| align="center" width="14.3%" | '''[[Casey Dunn|Dunn]]'''                <br/>(Phylogenomics & methods)
+
| align="left" width="60%" | [https://molevol.mbl.edu/images/7/73/MBL_WoodsHole_Aug10_2019_Part1.pdf Population genetics + selection I]  
| align="center" width="14.3%" | '''[[David Swofford|Swofford]]'''        <br/>([http://phylosolutions.com/paup-tutorial/ Model-selection tutorial])([http://paup.phylosolutions.com/ PAUP])
 
| align="center" width="14.3%" | '''[[John Huelsenbeck|Huelsenbeck]]'''  <br/>(Why I like ML & Bayes)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" style="background:#c8ccd1"  | '''17:00-19:00'''
+
| align="left" width="20%" | '''10:30 - 12:00'''
| align="center" width="14.3%" style="background:#F2E0CE | Welcome reception starts at 6PM
+
| align="left" width="20%" | [[Emilia Huerta-Sanchez|Huerta-Sanchez]]
| align="center" width="14.3%" colspan="5" style="background:#DCDCDC | Dinner break
+
| align="left" width="60%" | [https://molevol.mbl.edu/images/c/cc/MBL_WoodsHole_Aug10_2019_Part2.pdf Population genetics + selection II]
 
|-
 
|-
| align="center" width="14.3%" height="30" style="background:#c8ccd1" | '''19:00-20:30'''
+
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
| align="center" width="14.3%" style="background:#F2E0CE" | '''Welcome & opening reception''' <br/>'''[[:file:swope_terrace.jpg|Swope Bldg.]]'''
 
| align="center" width="14.3%" | '''[[Rachel Williams|Rachel Williams]]'''                          <br/> ([https://molevol.mbl.edu/index.php/Computer_lab_introduction '''Intro computer lab'''])
 
| align="center" width="14.3%" | '''[[Emily Jane McTavish|McTavish]]'''  <br/>([https://molevol.mbl.edu/images/d/d5/ML_search.pdf Maximum likelihood tree searching])
 
| align="center" width="14.3%" | '''[[Michael Landis|Landis]]'''      <br/>(Lecture: Graphical Models & RevBayes)
 
 
|-
 
|-
| align="center" width="14.3%" height="30" style="background:#c8ccd1"  | '''20:30-22:00'''
+
| align="left" width="20%" | '''14:00 - 15:30'''
| align="center" width="14.3%" style="background:#F2E0CE"  | '''Opening reception''' <br/>'''[[:file:swope_terrace.jpg|Swope Bldg.]]'''
+
| align="left" width="20%" | [[Emily Jane McTavish|McTavish]]
| align="center" width="14.3%" | '''[[Rachel Williams|Rachel Williams]]'''                          <br/> ([https://molevol.mbl.edu/index.php/Alignment_tutorial '''Alignment lab'''])
+
| align="left" width="60%" | [https://molevol.mbl.edu/images/7/77/Opentree_2019.pdf Open Tree of Life, gene-tree updating Slides]
| align="center" width="14.3%" | '''[[Emily Jane McTavish|McTavish]]'''  <br/>([https://mctavishlab.github.io/MLsearchLab Ascertainment bias & partition models])
 
| align="center" width="14.3%" | '''[[Tracy Heath|Heath]]'''      <br/>(Lecture: Divergence time estimation)
 
 
|-
 
|-
|}
+
| 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]
<!--
 
################ Second Week Edited #################
 
-->
 
 
 
== Second Week ==
 
 
 
 
 
{| border="1" width="100%"
 
|- style="background:SteelBlue"
 
| align="center" width="13.5%" |
 
| align="center" width="13.5%" style="color:white" | '''Monday'''<br/>(23 July)
 
| align="center" width="13.5%" style="color:white" | '''Tuesday'''<br/>(24 July)
 
| align="center" width="5%" style="color:white" | '''Wednesday'''<br/>(25 July)
 
| align="center" width="13.5%" style="color:white" | '''Thursday'''<br/>(26 July)
 
| align="center" width="13.5%" style="color:white" | '''Friday'''<br/>(27 July)
 
| align="center" width="13.5%" style="color:white" | '''Saturday'''<br/>(28 July)
 
| align="center" width="13.5%" style="color:white" | '''Sunday'''<br/>(29 July)
 
 
|-
 
|-
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''09:00-10:30'''
+
| align="left" colspan="3" style="background:#E5E7EC" | Dinner Break
| align="center" width="13.5%" | '''[[Bielawski|Bielawski]]'''    <br/>([http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/slides/WH2018_Parts1and2_Slides.pdf Drift, selection & codon models])
 
| align="center" width="13.5%" | '''[[Laura Eme|Laura Eme]]'''      <br/>(Substitution models for proteins)
 
| align="center" width="5%" style="background:#DCDCDC"|
 
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]'''    <br/>([https://peterbeerli.com/workshops/mbl/2016/talk1.pdf Introduction to the Coalescent])<br/> 
 
| align="center" width="13.5%" | '''[[Lacey Knowles|Knowles]]''' <br/>(Evolutionary applications of genomic data)
 
| align="center" width="13.5%" |  '''[[Michael Landis|Landis]]'''      <br/>(Lab: Phylogenetics w/ RevBayes) <br/>('''Room change:''' <br/>Loeb, G70)
 
| align="center" width="13.5%" |  [https://molevol.mbl.edu/index.php/Faculty '''Workshop faculty'''] <br/>(TBA) 
 
 
|-
 
|-
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''10:30-12:00'''
+
| align="left" width="20%" | '''19:00 - 20:30'''
| align="center" width="13.5%" | '''[[Bielawski|Bielawski]]'''<br/>([http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/slides/WH2018_Part3_slides.pdf Statistical analyses])
+
| align="left" width="20%" | [[Lacey Knowles|Knowles]]
([http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/slides/WH2018_Part4_slides.pdf Phenomenologcial load])
+
| align="left" width="60%" | Evolutionary applications of genomic data
| align="center" width="13.5%" | '''[[Laura Eme|Laura Eme]]'''      <br/>(Multi-gene phylogenetics:<br/>methods & applications)
 
| align="center" width="5%" style="background:#DCDCDC"|
 
| align="center" width="13.5%" | '''[[Laura Kubatko|Kubatko]]'''  <br/>(Species Tree Estimation)
 
| align="center" width="13.5%" | '''[[Lacey Knowles|Knowles]]''' <br/>(Evolutionary applications of genomic data)
 
| align="center" width="13.5%" | '''[[Michael Landis|Landis]]'''      <br/>(Lab: Phylogenetics w/ RevBayes)  <br/>('''Room change:''' <br/>Loeb, G70)
 
| align="center" width="13.5%" | '''Workshop faculty'''    <br/>(Participant discussions)
 
 
|-
 
|-
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''12:00-14:00'''
+
| align="left" width="20%" | '''20:30 - 22:00'''
| align="center" width="13.5%" colspan="7" style="background:#DCDCDC" | Lunch break
+
| align="left" width="20%" | [[Lacey Knowles|Knowles]]
 +
| align="left" width="60%" | Evolutionary applications of genomic data
 
|-
 
|-
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''14:00-15:30'''
+
| align="center" colspan="3" style="background:SteelBlue;color:white" | '''Sunday, August 11'''
| align="center" width="13.5%" | '''[[Belinda Chang|Chang]]'''<br/>([https://molevol.mbl.edu/images/3/33/Protein_Evolution_%26_Ancestral_Reconstruction.pdf Protein evolution & ancestral reconstruction])
 
| align="center" width="13.5%" | '''[[Bui Quang Minh|Bui Quang Minh]]'''<br/>(IQ-TREE)
 
| align="center" width="5%" style="background:#DCDCDC" |
 
| align="center" width="13.5%" | '''[[Laura Kubatko|Kubatko]]'''/'''[[David Swofford|Swofford]]''' <br/>(Species Tree Lab I)<br/>
 
| align="center" width="13.5%" | '''[[Cecile Ane|Cecile Ane]]'''  <br/>(Network models)
 
| align="center" width="13.5%" | '''[[Tracy Heath|Heath]]'''      <br/>(Lab: Divergence time estimation w/ RevBayes)
 
| align="center" width="13.5%"  style="background:#F2FFE6" | '''Open lab'''
 
 
|-
 
|-
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''15:30-17:00'''
+
| align="left" width="20%" | '''09:00 - 10:30'''
| align="center" width="13.5%" | '''[[Belinda Chang|Chang]]'''<br/>([https://molevol.mbl.edu/images/a/a3/Adaptive_Protein_Evolution.pdf Adaptive protein evolution])
+
| align="left" width="20%" | [[Mark Holder|Holder]]
| align="center" width="13.5%" | '''[[Bui Quang Minh|Bui Quang Minh]]'''<br/>(IQ-TREE)
+
| 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="5%" style="background:#DCDCDC" |
 
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]'''<br/>([https://peterbeerli.com/workshops/mbl/2016/talk2.pdf Extension of the basic coalescent])
 
| align="center" width="13.5%" |  '''[[Cecile Ane|Cecile Ane]]'''  <br/>(Network models)
 
| align="center" width="13.5%" | '''[[Tracy Heath|Heath]]'''      <br/>(Lab: Divergence time estimation w/ RevBayes)
 
| align="center" width="13.5%"  style="background:#F2FFE6" | '''Open lab'''
 
 
|-
 
|-
 +
| align="left" width="20%" | '''10:30 - 12:00'''
 +
| align="left" width="20%" | Workshop Faculty
 +
| align="left" width="60%" | Participant Discussions
 
|-
 
|-
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''17:00-19:00'''
+
| align="left" colspan="3" style="background:#E5E7EC" | Lunch Break
| align="center" width="13.5%" colspan="7" style="background:#DCDCDC" | Dinner break
 
 
|-
 
|-
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''19:00-20:30'''
+
| align="left" width="20%" | '''14:00 - 15:30'''
| align="center" width="13.5%" | '''[[Bielawski|Bielawski]]'''  <br/>([http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/lab.html PAML lab]) <br/>([http://awarnach.mathstat.dal.ca/~joeb/PAML_lab/resources/pamlDEMO_slides.pdf Lab slides])
+
| align="left" width="20%" | Open lab
| align="center" width="13.5%" style="background:#F2E0CE" | '''Course dinner party'''<br/>Lobster Boil, Terrace<br/>Starts at 6pm
+
| align="left" width="60%" |  
| align="center" width="5%" style="background:#DCDCDC" |
 
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]''' <br/>( [http://peterbeerli.com/workshops/mbl/2017/tutorial/ migrate tutorial])<br/>
 
| align="center" width="13.5%" | '''[[Scott Edwards|Edwards]]'''  <br/>(Lecture: Multilocus phylogeography and phylogenetics)
 
| align="center" width="13.5%" | '''[[Ben Evans]]''' <br/> Insights into how "important things" evolve
 
| align="center" width="13.5%" style="background:#DCDCDC" |
 
 
|-
 
|-
| align="center" width="13.5%" height="30" style="background:#c8ccd1" | '''20:30-22:00'''
+
| align="left" width="20%" | '''15:30 - 17:00'''
| align="center" width="13.5%" | '''[[Bielawski|Bielawski]]'''    <br/>([https://molevol.mbl.edu/index.php/PAML_notes Additional resources]) <br/>([https://bitbucket.org/EvoWorks/protocol-inference-of-episodic-selection/downloads/ Advanced lab])
+
| align="left" width="20%" | Open lab
| align="center" width="13.5%" style="background:#F2E0CE" |  '''Course dinner party'''
+
| align="left" width="60%" |  
| align="center" width="5%" style="background:#DCDCDC"| 
 
| align="center" width="13.5%" | '''[[Peter Beerli|Beerli]]''' <br/>( [http://peterbeerli.com/workshops/mbl/2017/tutorial/ migrate tutorial])
 
| align="center" width="13.5%" | '''[[Scott Edwards|Edwards]]'''  <br/>(Lecture: Multilocus phylogeography and phylogenetics)
 
| align="center" width="13.5%" style="background:#F2FFE6" | '''Open discussions & Graduation ceremony''' <br/>
 
| align="center" width="13.5%" style="background:#DCDCDC" |
 
 
|-
 
|-
 
|}
 
|}
 
<br/>
 
<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).