Session content

Monday – Classes from 2 to 8 pm Berlin time

 

Lecture: Introduction to Phylogenomics
- Phylogenetics pipeline overview
- Challenges
- Case studies

Lab: Orthology prediction
- De novo - Orthofinder
- Reference based orthologous inference

Lab: Sequence alignment / filtering
- Alignment with MAFFT
- Alignment visualization with AliView
- Alignment site filtering

 

 

 

Tuesday – Classes from 2 to 8 pm Berlin time

 

Lecture: Phylogenetic inference - Maximum parsimony, likelihood methods and substitution models

Lab: Phylogenetic inference methods
- Phylip or Paup
-RAxML/IQtree

 

 

 

Wednesday Classes from 2 to 8 pm Berlin time

 

Lecture: Bayesian inference - MCMC

Lab: Phylogenetic inference methods
Introduction to MCMC in R
- Bayesian phylogenetic inference - MrBayes

 

 

Thursday Classes from 2 to 8 pm Berlin time

 

Lecture: The Coalescent and its Implications - Introgression
- Incomplete lineage sorting
- Approximate vs. Likelihood based methods
- Concatenation versus the multi-species coalescent
- Identification of introgression

Lab: Gene-tree / Species-tree Approaches
- Maximum-likelihood species-tree inference with ASTRAL
- Bayesian species-tree inference with BPP

Lab: Introgression estimation
- Introgression tests based on D-statistics
- Introgression tests based on likelihood methods - BPP

 

 

 

 Friday Classes from 2 to 8 pm Berlin time

 

Lecture: Divergence times estimation

Lab: Divergence times estimation using MCMCTree and Beast