Ecology and Evolution [METAGENOMICS]
How can bioinformatics tools be employed to examine ecological niches?
- Create and interpret a multiple sequence alignment (e.g., T-COFFEE, MUSCLE, etc.).
- Describe the components of a phylogenetic tree (e.g., root, node, leaf).
- Explain the various types of phylogenetic trees (e.g., rooted, unrooted).
- Interpret a phylogenetic tree (e.g., which organism is most closely related to a given organism in the tree)
- Sketch a phylogenetic tree from its Newick representation.
- Use bootstrapping to assess the quality of a phylogenetic tree.
- Create a phylogenetic tree for a set of related sequences (nucleotide or amino acid) (e.g., MEGA).
- Use pre-existing tools to analyze a metagenomic data set to determine the set of organisms present in a metagenomic sample (e.g., 16s rRNA, Greengenes, mothur, etc.)