diff --git a/bio/pyfastaq/replace_bases/environment.linux-64.pin.txt b/bio/pyfastaq/replace_bases/environment.linux-64.pin.txt
index 51d72025eef..365a744dfba 100644
--- a/bio/pyfastaq/replace_bases/environment.linux-64.pin.txt
+++ b/bio/pyfastaq/replace_bases/environment.linux-64.pin.txt
@@ -1,28 +1,29 @@
 # This file may be used to create an environment using:
 # $ conda create --name <env> --file <this file>
 # platform: linux-64
+# created-by: conda 24.9.2
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.4.26-hbd8a1cb_0.conda#95db94f75ba080a22eb623590993167b
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_2.conda#fbe7d535ff9d3a168c148e07358cd5b1
+https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-7_cp313.conda#e84b44e6300f1703cb25d29120c5b1d8
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda#4222072737ccff51314b5ece9c7d6f5a
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#6305a3dd2752c76335295da4e581f2fd
-https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
-https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_2.conda#ea8ac52380885ed41c1baa8f1d6d2b93
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.0-h5888daf_0.conda#db0bfbe7dd197b68ad5f30333bae6ce0
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_2.conda#ddca86c7040dd0e73b2b69bd7833d225
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_1.conda#a76fd702c93cd2dfd89eff30a5fd45a8
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.0-h7b32b05_1.conda#de356753cfdbffcde5bb1e86e3aa6cd0
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-h4bc722e_0.conda#aeb98fdeb2e8f25d43ef71fbacbeec80
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.2-hee588c1_0.conda#93048463501053a00739215ea3f36324
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda#7dbaa197d7ba6032caf7ae7f32c1efa0
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.4-hd590300_0.conda#412ba6938c3e2abaca8b1129ea82e238
-https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.43.2-h2797004_0.conda#4b441a1ee22397d5a27dc1126b849edd
-https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
-https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-h2797004_0.conda#513336054f884f95d9fd925748f41ef3
-https://conda.anaconda.org/conda-forge/linux-64/python-3.12.0-hab00c5b_0_cpython.conda#7f97faab5bebcc2580f4f299285323da
-https://conda.anaconda.org/bioconda/noarch/pyfastaq-3.17.0-py_2.tar.bz2#e29b1d017dcd935969a388130335bfa6
-https://conda.anaconda.org/conda-forge/noarch/setuptools-68.2.2-pyhd8ed1ab_0.conda#fc2166155db840c634a1291a5c35a709
-https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.3-pyhd8ed1ab_0.conda#3fc026b9c87d091c4b34a6c997324ae8
-https://conda.anaconda.org/conda-forge/noarch/pip-23.3.1-pyhd8ed1ab_0.conda#2400c0b86889f43aa52067161e1fb108
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
+https://conda.anaconda.org/conda-forge/linux-64/python-3.13.3-hf636f53_101_cp313.conda#10622e12d649154af0bd76bcf33a7c5c
+https://conda.anaconda.org/conda-forge/noarch/pip-25.1.1-pyh145f28c_0.conda#01384ff1639c6330a0924791413b8714
+https://conda.anaconda.org/bioconda/noarch/pyfastaq-3.18.0-pyhdfd78af_0.tar.bz2#3b009c832acd828e64cce3b15d2fd93f
diff --git a/bio/pyfastaq/replace_bases/environment.yaml b/bio/pyfastaq/replace_bases/environment.yaml
index 861ae9fb77c..5c862f4c286 100644
--- a/bio/pyfastaq/replace_bases/environment.yaml
+++ b/bio/pyfastaq/replace_bases/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - pyfastaq =3.17.0
+  - pyfastaq =3.18.0