diff --git a/ChangeLog b/ChangeLog
index 34aae426..a0512159 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,13 @@
+Version 0.39.0 
+  * Fixed MAJOR ERRORS in assigning mutations to promoter regions of genes (#374)
+  * We are migrating the breseq documentation to the GitHub wiki. Please check there
+    for the most updated version. The docs packaged with breseq are sunsetting.
+  * Commands like breseq BAM2COV and BAM2ALN are now more forgiving in the ways regions can be specified.
+    * You can include commas in positions, which will be removed. REL606:627,165-627,185 instead of REL606:627,165-627,185
+    * You can provide just a single position REL606:627165 instead of REL606:627165-627165
+    * Hyphen-like characters (–) are automatically converted to hyphens (-).
+  * Removed an extra comma in gdtools COMPARE table output header (#368)
+
 Version 0.38.3
   * Miscellanous bug fixes related to nonstandard reference file loading.
   * Fixed problem adding --isescan-results with Genbank input to breseq CONVERT-REFERENCE.
diff --git a/configure.ac b/configure.ac
index 383a39af..2b98deae 100644
--- a/configure.ac
+++ b/configure.ac
@@ -19,7 +19,7 @@
 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
 AC_PREREQ([2.65])
-AC_INIT([breseq], [0.38.3], [jeffrey.e.barrick@gmail.com], [breseq], [http://barricklab.org/breseq])
+AC_INIT([breseq], [0.39.0], [jeffrey.e.barrick@gmail.com], [breseq], [http://barricklab.org/breseq])
 AC_CONFIG_AUX_DIR(aux_build)
 AC_CONFIG_MACRO_DIR([aux_build/m4])
 AC_CONFIG_HEADERS([aux_build/config.h])