Difference between revisions of "ISC-5935PPG"

 
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= ISC-5935PPG Practical Population genetic and Phylogenetic inference =
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= ISC-5935 Practical Population genetic and Phylogenetic inference =
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[[File:gracehopper.jpg|500px|left]]
 
This course is a tour de force discussing the theory behind 12 program packages and executions of tutorials.
 
This course is a tour de force discussing the theory behind 12 program packages and executions of tutorials.
[[File:studentswithcomputers.jpg|300px|left]]
 
== Goal ==
 
 
We learn about the details and pitfalls of inference software. The students will need to write short reports about data analyses using the discussed software, write short reviews of the reports, and also act as the scribe for the lectures.
 
We learn about the details and pitfalls of inference software. The students will need to write short reports about data analyses using the discussed software, write short reviews of the reports, and also act as the scribe for the lectures.
  
The schedule is only an example, check out the
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*[[ExposedPrograms | Program exposition and Tutorials]]
[[CandidatePrograms | Candidate Programs]] to figure out potential alternatives. If you have more suggestion email them to me.
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*[[practicalInferenceSyllabus | Syllabus]]
 
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*[[practicalInferenceSchedule | Schedule]]
== Current Schedule ==
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*[[CandidatePrograms | Candidate Programs]]
[this is work in progress]
 
<pre>
 
Programs:
 
1genepop
 
10beast phylogeny (snapp)
 
9beast skyline
 
8migrate divergence/migration
 
4dadi
 
2structure
 
13fastsimcoal2
 
15angsd
 
5treemix
 
? plink
 
11refbayes
 
6tess
 
12IMa
 
7Eigensoft
 
 
 
 
 
week dates
 
1   
 
    8/24  Intro and organisation
 
    8/26  Genepop/Isolation by distance/FST Scribe
 
    8/28  Tutorial   
 
2   
 
    8/31  Structure  Scribe
 
    --
 
    --
 
3   
 
    Labor day no class
 
    9/9  Tutorial 
 
    9/11  Tutorial  Report1
 
4   
 
    9/14  dadi Scribe
 
    9/16  Tutorial 
 
    9/18  Tutorial  Report2 Review1 
 
5   
 
    9/21  treemix  Scribe
 
    9/23  Tutorial
 
    9/25  Tutorial Report3 Review2
 
6   
 
    9/28  tess  Scribe
 
    9/30  Tutorial
 
    10/2  Tutorial  Report4 Review3
 
7   
 
    10/5  Eigensoft Scribe
 
    10/7  Tutorial
 
    10/9  Tutorial  Report5 Review4
 
8   
 
    10/12 Migrate  Scribe  Review5
 
    --    Self-tutorial
 
    --    Self-tutorial All write a short report
 
9   
 
    --    Finish writing report
 
    10/21 Migrate recap: Discussion about how to write a self-guided tutorial
 
    10/23 Beast skyline  Scribe
 
10 
 
    10/26 Tutorial
 
    10/28 Beast SNAPP  Scribe
 
    10/30 Tutorial  Report6
 
11 
 
    11/2  refbayes  Scribe
 
    11/4  Tutorial
 
    11/6  Tutorial  Report7 Review6
 
12 
 
    11/9  IMa    Scribe
 
    --    Self-tutorial
 
    --    Compare to migrate using a simulated dataset
 
13 
 
    --    ALL: write a short report abot the migrate-ima comparison
 
    11/18 fastsimcoal2  Scribe
 
    11/20 Tutorial 
 
14 
 
    11/23 Tutorial  Report8 Review7
 
    Thanksgiving
 
    Thanksgiving
 
15 
 
    11/30 angsd    Scribe Review8
 
    12/2  Tutorial
 
    12/4  Tutorial 
 
finals week
 
</pre>
 

Latest revision as of 05:29, 25 August 2015

ISC-5935 Practical Population genetic and Phylogenetic inference

Gracehopper.jpg

This course is a tour de force discussing the theory behind 12 program packages and executions of tutorials. We learn about the details and pitfalls of inference software. The students will need to write short reports about data analyses using the discussed software, write short reviews of the reports, and also act as the scribe for the lectures.