Update 1.5.2_Viral_Taxonomy_and_Phylogeny_II.md

Author: vmkhot

_episodes/1.5.2_Viral_Taxonomy_and_Phylogeny_II.md

@@ -79,14 +79,16 @@ Instead, you could post-process the tree using the `ete3` library in Python.
 
 > ## Exercise -  Post-process large tree --> smaller tree
 > 
-> There are a few ways to post-process trees to make them viewable or to highlight our viruses of interest.  
-> One way would be build a script that takes the input of a single contig and the tree file and pruning the tree around the contig to a certain number of the closest reference viruses. Pruning a tree means only certain clades or leaves are left.  
-> Instead of pruning, you can also "collapse" clades to make the tree manageable to view. For this, clades are collapsed into a single leaf that replaces them. In very large trees, you will probably encounter large clades that are far away from your sequences of interest that can be collapsed and replace. For this, you might want to give an input of all your viruses of interest. 
-> The `ete3` library is a really useful resource to process trees. 
+> There are a few ways to post-process trees to make them viewable or to highlight our viruses of interest.
+> 
+> - One way would be build a script that takes the input of a single contig and the tree file and pruning the tree around the contig to a certain number of the closest reference viruses. Pruning a tree means only certain clades or leaves are left.  
+> - Instead of pruning, you can also "collapse" clades to make the tree manageable to view. For this, clades are collapsed into a single leaf that replaces them. In very large trees, you will probably encounter large clades that are far away from your sequences of interest that can be collapsed and replace. For this, you might want to give an input of all your viruses of interest. 
+>
 >{: .source}
 {: .challenge}
 
 We've built two python scripts using this library to shrink the size of tree outputs. The locations of the tree-pruning scripts will be in your python_scripts directory `python_scripts/1.5_collapse_non_target_clades.py` and `python_scripts/1.5_trim_tree_to_500_neighbors.py`.  
+
 `1.5_trim_tree_to_500_neighbors.py` will trim your tree around a contig of your choice. `1.5_collapse_non_target_clades.py` will collapse clades that don't contain viruses from our dataset. These scripts also include a section to generate ITOL annotation files. 
 
 > ## python script to trim tree around 1 contig