diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md
index f44356d..89998be 100644
--- a/PhyloToL-Part-1:-GF-assignment.md
+++ b/PhyloToL-Part-1:-GF-assignment.md
@@ -92,9 +92,20 @@ Available parameters are:
 | --maxlen  |int|-| Maximum transcript length | 
 | --seq_count  |int|-| minimum number of sequences after assigning OGs | 
 
-#### To run the PhyloToL part 1 for both processing transcriptomes and removing sequences that resulted from index switching (cross plate contamination), run (LAk and ACL): 
+
+####Index Switching (Cross plate contamination)
+As you run PhyloToL part 1 on transcriptomes, you might want to remove sequences from your assembled transcripts that are a result of index switching. This is done by (LAK and ACL on XPC removal process with conspecific file). To include this parameter to your PhyloToL part 1 run, you will need to add the '--xplate_contam --conspecific_names Conspecific.txt' flag to the command line as follow:
+
 `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases --xplate_contam --conspecific_names Conspecific.txt > log.txt`
 
+Example of a Conspecific.txt file
+ | Taxa  | plate | 
+| —------------  | —------------------ | 
+| EE_uc_Me04  | Metatranscriptome | 
+| EE_uc_Me05  | Metatranscriptome | 
+| EE_uc_Me06  | Metatranscriptome | 
+| EE_uc_Me07  | Metatranscriptome | 
+
 
 
 ### Processing genomes