ISC-5935PPG
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.
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.
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