This module is part of the Microbial Genomics course at the MSc Bioinformatics and Biocomplexity at Utrecht University.
Here, we aim to introduce students to basic concepts in Phylogenomics, exploring the effects of known phylogenomics artefacts to identify best practices. Some of the main concepts in this module include gene marker selection, concatenation strategy, the effects of alignment treatments, and species tree interpretation.
This exercise will be complemented by short lectures on:
- Introduction to this assignment
- Molecular phylogenetics
- How to reconstruct a species tree
- Frontiers in phylogenomics and tree of life exploration
- Final discussion
Today's exercise consists of the following sections:
- 01: Background
- 02: Data
- 03: Alignment
- 04: Concatenation and Phylogeny
- 05: Single-gene trees
- 06: A concatenated subset
- 07: Recoding
- Bonus: Higher quality alignments