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compgenomics:modul1 [2025/05/16 07:08] – [Analysis] felixcompgenomics:modul1 [2025/09/23 13:09] (current) – felix
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 === Task 2: How are they related to each other? === === Task 2: How are they related to each other? ===
  
-  - Extract the information from the "taxid" column and save it in a ''.txt'' file+  - 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**)   - 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
  
 ---- ----
  
 [[:compgenomics|Back to main]] [[:compgenomics|Back to main]]