ForBio Phylogenomics

A collection of tutorials to be covered in the ForBio Phylogenomics course. Each day we will begin at 9 am and end at around 5:30 pm. In between, we will have lunch break. It depends a little bit on the progress during the morning session, but it is planned to be between 1:00 pm and 1:30 pm. Each session will consists of lectures and practical exercises, except for the very first one, which does not have practical exercises.

Prepration

• Requirements<br>A list of all installations required for the tutorials

• Getting Started<br>General instructions on the use of these tutorials

Week 1

Monday

• Introduction into the course<br>An introduction to the course and the first step of the phylogenetic analyses we will build upon (no exercises)

• Sources of incongruence & Contamination screening<br>General lectures on inconrguence and a tutorial on the detection of contamination in datasets using a metabarcoding-based approach.

Tuesday

• Paralogy screening after orthology determination<br>A tutorial on the detection of paralogy in datasets using a single trees, bootstrap support and reference databases.

• Missing data and low phylogenetic signal<br>A tutorial on reducing missingness and detecting low phylogenetic signal in the data.

Wednesday

• Determination of rogue taxa<br>A tutorial on the detection of rogue taxa in datasets using different approaches.

• Model misspecification and partitioning<br>A tutorial on reducing model misspecifications by using partitioning schemes.

Thursday

• Saturation<br>A tutorial on the detection of saturation in phylogenomic datasets.

• Base composition heterogeneity<br>A tutorial on the detection of base composition heterogeneity in phylogenomic datasets.

Friday

• Branch length heterogeneity 1<br>A tutorial on the visualization of branch length heterogeneity in phylogenomic datasets.

• Branch length heterogeneity 2<br>A tutorial on the detection of branch length heterogeneity in phylogenomic datasets.

Week 2

Monday

• Bayesian Phylogenetic Inference<br>A tutorial on Bayesian inference of time-calibrated phylogenies

• Phylogenetic Divergence-Time Estimation<br>A tutorial on phylogenetic divergence-time estimation with with fossils

Tuesday

• Maximum-Likelihood Species-Tree Inference<br>A tutorial on maximum-likelihood species-tree inference based on gene trees

• Bayesian Species-Tree Inference<br>A tutorial on Bayesian inference of time-calibrated species trees

• Whole-Genome Alignment<br>A tutorial on repeat masking and whole-genome alignment of assembled genomes

Wednesday

• Species-Tree Inference with SNP Data<br>A tutorial on the inference of species trees from SNP data based on quartets

• Divergence-Time Estimation with SNP Data<br>A tutorial on Bayesian divergence-time estimation with SNP data

• Maximum-Likelihood Inference of Species Networks<br>A tutorial on maximum-likelihood phylogenetic inference of species networks

• Bayesian Inference of Species Networks<br>A tutorial on Bayesian phylogenetic inference of species networks

Thursday

• Analysis of Introgression with SNP Data<br>A tutorial on the analysis of hybridization and introgression with SNP data

• Analysis of Introgression with Tree Topologies<br>A tutorial on the analysis of hybridization and introgression with tree topologies from across the genome.

Friday

• Inference from Simulated Data<br>A tutorial on coalescent simulations of genomic data and inferences from simulated data

Exam

• The Inference from Simulated Data on Friday of the second week will also serve as our examination for this course as different analyses throughout the course have to be recapitulated by the student using simulated data instead of empirical ones. Hence, the different causes are known. The final part will be that the students have to present their results at the end for passing the course.