diff --git a/README.md b/README.md
index b07f1bf..d479c3b 100644
--- a/README.md
+++ b/README.md
@@ -242,7 +242,8 @@ Options:
                        Input filenames must meet these conditions:
                             - Contain a unique identifier at the beginning of the name (e.g. EcoliBW25113);
                             - Contain the string "cds" after the unique identifier;
-                            - End with the extension .fna (PUPpy automatically only uses such files in the given folder).
+                            - End with the extension .fna (PUPpy automatically only uses such files in the given folder);
+                            - Must NOT contain hyphens (-) in the filename as they cause unintended behavior.
                        A filename example is: "EcoliBW25113_cds.fna". For more detailed instructions, please refer to the PUPpy GitHub documentation.
   -nt, --nonTarget     Directory with CDS files of non-targets in the defined microbial community, for specificity checks.
   -o, --outdir         Relative path to the output folder. Default: Align_OUT.
@@ -277,7 +278,8 @@ Options:
                                Input filenames must meet these conditions:
                                     - Contain a unique identifier at the beginning of the name (e.g. EcoliBW25113);
                                     - Contain the string "cds" after the unique identifier;
-                                    - End with the extension .fna (PUPpy automatically only uses such files in the given folder).
+                                    - End with the extension .fna (PUPpy automatically only uses such files in the given folder);
+                                    - Must NOT contain hyphens (-) in the filename as they cause unintended behavior.
                                A filename example is: "EcoliBW25113_cds.fna". For more detailed instructions, please refer to the PUPpy GitHub documentation.  
   -i, --input                  Input file (ResultDB.tsv) from `puppy-align` or UniqueGenesList.tsv. Required.
   -o, --outdir                 Output directory for primer design files. Default: 'Primer3_output'.
diff --git a/scripts/puppy-align b/scripts/puppy-align
index 8074d5e..4ec809b 100644
--- a/scripts/puppy-align
+++ b/scripts/puppy-align
@@ -68,7 +68,8 @@ Options:
                        Input filenames must meet these conditions:
                             - Contain a unique identifier at the beginning of the name (e.g. EcoliBW25113);
                             - Contain the string "cds" after the unique identifier;
-                            - End with the extension .fna (PUPpy automatically only uses such files in the given folder).
+                            - End with the extension .fna (PUPpy automatically only uses such files in the given folder);
+                            - Must NOT contain hyphens (-) in the filename as they cause unintended behavior.
                        A filename example is: "EcoliBW25113_cds.fna". For more detailed instructions, please refer to the PUPpy GitHub documentation.
   -nt, --nonTarget     Directory with CDS files of non-targets in the defined microbial community, for specificity checks.
   -o, --outdir         Relative path to the output folder. Default: Align_OUT.
diff --git a/scripts/puppy-primers b/scripts/puppy-primers
index 7fa2d0c..ac7b11d 100644
--- a/scripts/puppy-primers
+++ b/scripts/puppy-primers
@@ -77,7 +77,8 @@ Options:
                                Input filenames must meet these conditions:
                                     - Contain a unique identifier at the beginning of the name (e.g. EcoliBW25113);
                                     - Contain the string "cds" after the unique identifier;
-                                    - End with the extension .fna (PUPpy automatically only uses such files in the given folder).
+                                    - End with the extension .fna (PUPpy automatically only uses such files in the given folder);
+                                    - Must NOT contain hyphens (-) in the filename as they cause unintended behavior.
                                A filename example is: "EcoliBW25113_cds.fna". For more detailed instructions, please refer to the PUPpy GitHub documentation.  
   -i, --input                  Input file (ResultDB.tsv) from `puppy-align` or UniqueGenesList.tsv. Required.
   -o, --outdir                 Output directory for primer design files. Default: 'Primer3_output'.