Updated Set up (markdown)

Set-up.md

@@ -1,5 +1,4 @@
 ## Transcriptomes
-* Assembled transcripts
 ### What you need in Transcriptomes folder:
 * A folder called “AssembledTranscripts” with your assembled transcript fasta files
 * A folder called “Databases” with the three folders:
@@ -16,3 +15,20 @@
 * *A file called “Conspecific.txt” filled with your 10-digit codes in a column tab separated with the conspecific (e.g. genus, species or metatranscriptome) names for each sample
 
 *not required for all PhyloToL runs
+
+## Genomes
+### What you need in Genomes folder:
+* A folder called “CDS” with your CDS files
+* A folder called “Databases” with the three folders:
+  * db_BvsE (how we ID likely-bacterial sequences)
+  * db_StopFreq (for stop codon assignment)
+  * db_OG (this must be current version of the hook)
+    * Current version is Hook-6.6 (08/04/23)
+    * Files needed:
+      * Hook *.dmnd file ([Current version Hook-6.6.dmnd](https://drive.google.com/open?id=1ywYLZXzcTERDFCysz5vPbI9u6WRxz5r0&usp=drive_copy))
+      * Hook *.fasta file ([Current version Hook-6.6.fasta](https://drive.google.com/open?id=1AN4_SmZUYFH6_xh2qOhyNUlFZ_NT9_-D&usp=drive_copy))
+* A folder called “Scripts” filled with the 10 scripts from [here on Github](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts)
+* *A file called “Gcodes.txt” filled with your 10-digit codes in a column tab separated with the genetic code designation for each sample
+  * NOTE that this step is only if you are running genomes that all need specific genetic codes!
+
+*not required for all PhyloToL runs