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--- compgenomics:modul1 [2025/05/16 07:05] – [Analysis] felix
+++ compgenomics:modul1 [2025/05/16 07:24] (current) – [Analysis] felix
@@ Line 10: / Line 10: @@
 <WRAP round tip 500px center>
-All species are related to each other, and this relationship can be represented by a tree
+**Assumption**: All species are related to each other, and this relationship can be represented by a tree
 </WRAP>
@@ Line 26: / Line 26: @@
 === 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
 ----
 [[:compgenomics|Back to main]]