ISC-5935PPG

Revision as of 18:22, 17 August 2015 by Beerli (talk | contribs) (→‎Goal)

ISC-5935PPG Practical Population genetic and Phylogenetic inference

This course is a tour de force discussing the theory behind 12 program packages and executions of tutorials.

Studentswithcomputers.jpg

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.

The schedule is only an example, check out the Candidate Programs to figure out potential alternatives. If you have more suggestion email them to me.

Current Schedule

[this is work in progress]

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