Updated QuickStart EukPhylo (markdown)

QuickStart-EukPhylo.md

@@ -182,7 +182,7 @@ Below are several optional ways to parameterize EukPhylo Part 2
 ## Contamination Removal 
 Contamination removal within EukPhylo (also called Contamination Loop) allows for sequence removal based on Sisters/Subsisters identification or based on Clades diversity. An examplar run is available in [Figshare](https://figshare.com/articles/dataset/Examplar_runs_PhyloToL_and_CLoop/26662018)
 
-### Set up 
+### Set up:
 * An input folder (called for example Input), with both 
     * the treefiles 
     * the fasta files matching the trees
@@ -191,7 +191,7 @@ Contamination removal within EukPhylo (also called Contamination Loop) allows fo
 * a txt file containing the rules for contamination removal
 * the Scripts Folder
 
-### Running
+### Running:
 Basic running of the Contamination loop, with the sister mode:
 
 `python3 Scripts/eukphylo.py  --start trees --end trees --data Input --output Output --contamination_loop seq --sister_rules sister_rules_file.txt  > log.out`
@@ -215,11 +215,11 @@ Options:
 | --cl_exclude_taxa | no | Any valid path | Path to a file containing taxon names present in input MSA/tree files but which should be removed in the first iteration of the contamination loop. | none |
 
 
-## Concatenation:
+## Concatenation
 
 EukPhylo includes an option to choose orthologs and produce a concatenated alignement.
 
-### Set up
+### Set up:
 * A folder called `Output` containing all outputs from the main pipeline (with Guidance, Trees, Pre-Guidance, NotGapTrimmed folders)
 * the Scripts folder
 * a list of taxa to concatenate