diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md
index 608995b..f71ada9 100644
--- a/PhyloToL-Part-1:-GF-assignment.md
+++ b/PhyloToL-Part-1:-GF-assignment.md
@@ -71,10 +71,8 @@ Replacing the PhyloToL Hook DB with a user-defined set of gene families is strai
 Role of each script
 <img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Transcriptomes_scripts.png" width="100%">
 
-* **Main inputs** : The main inputs for processing transcriptomes are: a folder containing the assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData) (as described above), a folder containing the Databases with three subfolders(db_BvsE (how we ID likely-bacterial sequences), db_StopFreq (for stop codon assignment), and db_OG (this must be current version of the hook)), and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts).
-* **Outputs** : The main outputs after processing transcriptomes are: ReadyToGo files which contain the nucleotide and amino acid sequences of each taxa, and a summary information of the sequences processed for each taxa.
-
-#### To run the PhyloToL part 1 for processing transcriptomes, run:
+Running PhyloToL Part 1 on transcriptomes requires at least 3 items in your main directory: 1) A folder named Scripts and containing all [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts) from PhyloToL part 1 github, 2) a folder containing your assembled [transcripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/TestData) (as described above), and 3) a folder containing the Databases with three subfolders(db_BvsE (how we ID likely-bacterial sequences), db_StopFreq (for stop codon assignment), and db_OG (The hook database as described above)).  Default script starts with assembled transcripts and produces ReadyToGo files (nucleotide and amino acid sequences) of each taxa, and a summary information of the sequences processed for those taxa. 
+* To run the PhyloToL part 1 for processing transcriptomes, run:
  `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases > log.txt`
 
 Available parameters are:
@@ -112,8 +110,8 @@ Example of a Conspecific.txt file
 Role of each script
 <img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Genomes_scripts.png" width="100%">
 
-* **Main inputs** : The main inputs for processing genomes are: a folder containing the assembled [CDS](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/TestData), a folder containing the Databases with three subfolders(db_BvsE (how we ID likely-bacterial sequences), db_StopFreq (for stop codon assignment), and db_OG (this must be current version of the hook)), and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts).
-* **Outputs** : The main outputs after processing genomes are: ReadyToGo files which contain the nucleotide and amino acid sequences of each taxa, and a summary information of the sequences processed for each taxa.
+Running PhyloToL Part 1 on genomes requires at least 3 items in your main directory: 1) A folder named Scripts and containing all [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts) from PhyloToL part 1 github, 2) a folder containing your assembled [CDS](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/TestData) (as described above), and 3) a folder containing the Databases with three subfolders(db_BvsE (how we ID likely-bacterial sequences), db_StopFreq (for stop codon assignment), and db_OG (The hook database as described above)).  Default script starts with assembled transcripts and produces ReadyToGo files (nucleotide and amino acid sequences) of each taxa, and a summary information of the sequences processed for those taxa. 
+
 
 #### To run the PhyloToL part 1 for processing genomes, run:
  `python Scripts/wrapper.py --first_script 1 --last_script 5 --cds CDS --output . --genetic_code Gcode.txt --databases Databases > log.txt`