diff --git a/HISTORY.md b/HISTORY.md
index e691c83..f9cfb63 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -1,5 +1,9 @@
 # History
 
+1.3.1 (2026-07-20)
+------------------
+* `phold citation` now also prints our [protocols paper](https://doi.org/10.1002/cpz1.70405) citation alongside the existing Phold citation
+
 1.3.0 (2026-07-02)
 ------------------
 * Adds multi-GPU support - use `--gpus` (e.g. `--gpus 0,2`) to specify which CUDA device indices `phold` and Foldseek-GPU should use. Defaults to all visible CUDA GPUs. Has no effect on MPS/XPU systems
diff --git a/pyproject.toml b/pyproject.toml
index c5f89a8..954759f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ requires = ["setuptools>=61.0", "wheel>=0.37.1"]
 [project]
 # https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
 name = "phold"
-version = "1.3.0" # change VERSION too
+version = "1.3.1" # change VERSION too
 description = "Phage Annotations using Protein Structures"
 readme = "README.md"
 requires-python = ">=3.8, <4"
diff --git a/src/phold/utils/CITATION b/src/phold/utils/CITATION
index aec1520..2ab2be3 100644
--- a/src/phold/utils/CITATION
+++ b/src/phold/utils/CITATION
@@ -1,2 +1,6 @@
 Bouras G, Grigson SR, Mirdita M, Heinzinger M, Papudeshi B, Mallawaarachchi V, Green R, Kim SR, Mihalia V, Psaltis AJ, Wormald P-J, Vreugde S, Steinegger M, Edwards RA: "Protein Structure Informed Bacteriophage Genome Annotation with Phold", Nucleic Acids Research, Volume 54, Issue 1, 13 January 2026, gkaf1448, https://doi.org/10.1093/nar/gkaf1448
 
+Please also consider citing our protocols paper:
+
+Bouras G, Grigson SR, Durr L, Papudeshi B, Mallawaarachchi V, Vreugde S, Edwards RA: "Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny", Current Protocols, Volume 6, Number 7, 6 July 2026, https://doi.org/10.1002/cpz1.70405
+
diff --git a/src/phold/utils/VERSION b/src/phold/utils/VERSION
index 7e099ec..6261a05 100644
--- a/src/phold/utils/VERSION
+++ b/src/phold/utils/VERSION
@@ -1 +1 @@
-1.2.6
\ No newline at end of file
+1.3.1
\ No newline at end of file