diff --git a/README.md b/README.md
index dc96ba8b..0a19c157 100644
--- a/README.md
+++ b/README.md
@@ -31,7 +31,7 @@ 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/v0.9.28/diamond-linux64.tar.gz
+    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.29/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 1d556b95..3d6467ea 100644
Binary files a/diamond_manual.pdf and b/diamond_manual.pdf differ
diff --git a/src/ChangeLog b/src/ChangeLog
index e1e7c4f3..31eb4f8f 100644
--- a/src/ChangeLog
+++ b/src/ChangeLog
@@ -1,5 +1,5 @@
 [0.9.29]
-- Fixed a bug that could cause taxonomy features to function incorrectly, affecting versions 0.9.27 and 0.9.28.
+- Fixed a bug that could cause taxonomy features to function incorrectly for databases created by versions 0.9.27 and 0.9.28.
 
 [0.9.28]
 - Fixed a bug that could cause alignment score overflows for scores > 65535 in frameshift alignment mode.
diff --git a/src/basic/basic.cpp b/src/basic/basic.cpp
index 5bf49624..fc2cefb7 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 = "0.9.28";
+const char* Const::version_string = "0.9.29";
 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 2831a77b..3df82a6b 100644
--- a/src/basic/const.h
+++ b/src/basic/const.h
@@ -23,7 +23,7 @@ struct Const
 {
 
 	enum {
-		build_version = 129,
+		build_version = 130,
 		seedp_bits = 10,
 		seedp = 1<<seedp_bits,
 		max_seed_weight = 32,