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compgenomics:modul1 [2025/05/16 06:59] – [Module 1: Datasets] felixcompgenomics:modul1 [2025/09/23 13:09] (current) – felix
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-<WRAP round help 350px>+<WRAP round help 500px center>
 What species are available for my analysis and how are they related to each other? What species are available for my analysis and how are they related to each other?
 </WRAP> </WRAP>
  
 +----
  
- +<WRAP round tip 500px center> 
-<WRAP round tip> +**Assumption**: All species are related to each other, and this relationship can be represented by a tree
-All species are related to each other, and this relationship can be represented by a tree+
 </WRAP> </WRAP>
 +
 +
 ==== Analysis ==== ==== Analysis ====
  
-=== Task 1 ===+=== Task 1: What species are available for my analysis?  ===
  
   - Go to [[https://www.ncbi.nlm.nih.gov/datasets/|NCBI Datasets]]   - Go to [[https://www.ncbi.nlm.nih.gov/datasets/|NCBI Datasets]]
   - Search for all available eukaryotic genomes   - Search for all available eukaryotic genomes
   - Filter for genomes "with [[https://www.ncbi.nlm.nih.gov/refseq/about/|RefSeq]] Annotation"   - 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<WRAP>
 +<hidden SPOILER>
 +[[compgenomics:modul1:taxidfile|Download file with taxids from here]]
 +</hidden></WRAP>
 +  - 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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