Update file phylo_exercise.md

exercises/phylo_exercise.md

@@ -203,6 +203,21 @@ Change the variables to your needs.
 
 
 
+### DOWNLOAD TREE FILES
+
+The complete output for the SNP calling, MSA and tree can be found here, download it into a `[target_directory]` of your choice. 
+
+```bash
+# Typestrain as reference
+cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/03_output_mrsa/snippy_ref_typestrain [target_directory]
+
+# Hybrid assembly as reference
+cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/03_output_mrsa/snippy_ref_hybrid [target_directory]
+```
+
+
+
+