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@@ -12,4 +12,22 @@ We provide a diverse database of 1,000 genomes and transcriptomes from across th
 
 # Contamination loop
 
-The Contamination Loop is implemented within PhyloToL to allow the removal of contaminants based on the topology of each tree (= Phylogenetic based contamination removal). 3 modes are available and described in this section: ‘sister’, ‘subsister’ and ‘clade’. All modes take a user defined rules file to identify the sequences to remove. 
+The contamination coop (CL) is implemented within PhyloToL to allow the removal of contaminants based on the topology of each tree (phylgoeny-informed contamination removal). Three modes are available: sister-, subsister-, and clade-based contamination removal. All modes take a user defined file of 'rules,' used to identify the sequences to remove. 
+
+Sisters-based contamination removal identifies sequences as putative contaminants based on their sister relationships. If a sequence from sample A appears on a tree sister to a sequence from sample B, and sample B is known to have contaminated sample A, then the sequence from sample A will be removed. Subsisters-based removal operates similarly, but looks at the taxa that are sister to sample A's _parent_ node, useful for when multiple samples are contaminated by the same other sample.
+
+Clade-based contamination removal operates differently. In this mode, the CL searches for monophyletic clades in each gene tree that match a set of given criteria. For example, if we want to 'clade-grab' for robust Opisthokont clades, we might choose to keep only Opisthokont sequences that fall in a monophyletic clade of 12 or more species of Opisthokont; all other Opisthokont sequences in the tree would be removed.
+
+## Setup
+
+The CL requires 1) a folder of alignments (not gap trimmed) and 2) a folder of gene trees in order to run, and they should be formatted in the same way as output by the preceding steps of PhyloToL part 2 (i.e. in the "Output" folder, see above). You can also give it data _not_ output by PhyloToL, but you will need to match the folder, file, and sequence name formats.
+
+You will also need to create a 'rules' file. The format here varies between the different modes of the CL.
+
+## Running
+
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+