diff --git a/Set-up.md b/Set-up.md
index 570f548..3d29d34 100644
--- a/Set-up.md
+++ b/Set-up.md
@@ -1,7 +1,7 @@
 ## Transcriptomes
 ### What you need in Transcriptomes folder:
-* A folder called “<font color="orange">AssembledTranscripts</font>” with your assembled transcript fasta files
-* A folder called “Databases” with the three folders:
+* A folder called “**AssembledTranscripts**” with your assembled transcript fasta 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)
@@ -9,17 +9,17 @@
     * 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 14 scripts from [here on Github](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/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
+* A folder called “**Scripts**” filled with the 14 scripts from [here on Github](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/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 transcriptomes that all need specific genetic codes!
-* *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
+* *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:
+* 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)
@@ -27,8 +27,8 @@
     * 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
+* 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
\ No newline at end of file