Discussion of Fridays's lab

Questions to comtemplate:

• Where do support values go if one draws a tree?
• How to test which model is most appropriate.
• Tree space is gigantic -> heuristic searches (NNI SPR TBR)
• Is a general time reversible model appropriate (is the composition of sequences homogeneous)?
• What data to use? (nucleotides -> recoded as R/Y?, aa -> recoded into Dayhof groups, codons (61x61 substitution matrix)
• Advantages and disadvantages to exclude positions with gaps.
• Programs frequently used phyml (seaview), Raxml, iQtree, MrBayes, fasttree

PPT Slides for today (continuation from last Wednesday)

If time, start overview on population genetics