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How can bioinformatics tools be employed to examine ecological niches?

Topic

Ecology and Evolution [METAGENOMICS]

Framing Question

How can bioinformatics tools be employed to examine ecological niches?

Learning Objectives

  • 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.)

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