===== Module 1: Datasets ====



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What species are available for my analysis and how are they related to each other?
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**Assumption**: All species are related to each other, and this relationship can be represented by a tree
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==== Analysis ====

=== Task 1: What species are available for my analysis?  ===

  - Go to [[https://www.ncbi.nlm.nih.gov/datasets/|NCBI Datasets]]
  - Search for all available eukaryotic genomes
  - Filter for genomes "with [[https://www.ncbi.nlm.nih.gov/refseq/about/|RefSeq]] Annotation"
  - Add column "taxid"
  - Download table in CSV format

=== Task 2: How are they related to each other? ===

  - Extract the information from the "taxid" column and save it in a ''.txt'' file
  - Go to [[https://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi|NCBI CommonTree]] and upload your ''.txt'' file (-> menu: **Add from file**)
  - Download the tree in Phylip format (-> menu: **save as -> phylip tree**)
  - Open the [[https://itol.embl.de/|iTOL web page]]
  - Upload the tree into iTOL and explore:
    - How many animals, how many fungi, how many plants are there? (<wrap tip>Tip:</wrap> the nodes in the tree will be named according to entries in [[https://www.ncbi.nlm.nih.gov/taxonomy|NCBI Taxonomy]])
    - Highlight these three clades with different colors
    - Compare the circular vs rectangular representation of the tree

=== Summary and discussion ===

  * Note down your observations and questions
  * Discuss with the group

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