diff --git a/README.md b/README.md
index ce10d0c9..6e2335d8 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@ quick example for setting up and using the program on Linux.
 Installing the software on your system may be done by downloading it in
 binary format for immediate use:
 
-    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.24/diamond-linux64.tar.gz
+    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.25/diamond-linux64.tar.gz
     tar xzf diamond-linux64.tar.gz
 
 The extracted `diamond` binary file should be moved to a directory
diff --git a/diamond_manual.pdf b/diamond_manual.pdf
index 9a93ec6d..61c4fbfb 100644
Binary files a/diamond_manual.pdf and b/diamond_manual.pdf differ
diff --git a/src/ChangeLog b/src/ChangeLog
index 2e6b09e9..086d3605 100644
--- a/src/ChangeLog
+++ b/src/ChangeLog
@@ -1,14 +1,16 @@
 [0.9.25]
-- Added support for the sscinames output field to print subject scientific names to the tabular output format.
+- Added support for the `sscinames` output field to print subject scientific names to the tabular output format.
 - Fixed a compiler error for GCC 8.2.
-- Added option --stop-match-score to set the match score of stop codons.
-- Fixed a bug that caused the qqual output field to not be correctly clipped to the aligned part of the query.
-- Added output fields qseq_gapped and sseq_gapped to the tabular format.
+- Added option `--stop-match-score` to set the match score of stop codons.
+- Fixed a bug that caused the `qqual` output field to not be correctly clipped to the aligned part of the query.
+- Added output fields `qseq_gapped` and `sseq_gapped` to the tabular format.
 - Raised compiler requirement to GCC 4.8.
 - Fixed a bug that caused the final sequence positions to not be printed in the pairwise format.
-- Allow using --min-score instead of --top for the LCA computation of the taxonomy output format.
+- Allow using `--min-score` instead of `--top` for the LCA computation of the taxonomy output format.
 - Reduced the number of temporary files.
 - Added output field `qstrand` to the tabular format.
+- Database format version changed to 3.
+- Fixed a bug in the `--range-culling` mode that could cause undefined behaviour.
 
 [0.9.24]
 - Fixed a compiler error on macOS.
diff --git a/src/basic/basic.cpp b/src/basic/basic.cpp
index a3b3ff86..04de5a46 100644
--- a/src/basic/basic.cpp
+++ b/src/basic/basic.cpp
@@ -24,7 +24,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "sequence.h"
 #include "masking.h"
 
-const char* Const::version_string = "0.9.24";
+const char* Const::version_string = "0.9.25";
 const char* Const::program_name = "diamond";
 const char* Const::id_delimiters = " \a\b\f\n\r\t\v\1";
 
diff --git a/src/basic/const.h b/src/basic/const.h
index 64e181d8..24f94c1c 100644
--- a/src/basic/const.h
+++ b/src/basic/const.h
@@ -23,7 +23,7 @@ struct Const
 {
 
 	enum {
-		build_version = 125,
+		build_version = 126,
 		seedp_bits = 10,
 		seedp = 1<<seedp_bits,
 		max_seed_weight = 32,