diff --git a/PhyloFlash.pm b/PhyloFlash.pm
index 7917017..bf98ed4 100644
--- a/PhyloFlash.pm
+++ b/PhyloFlash.pm
@@ -28,7 +28,7 @@ This module contains helper functions shared by the phyloFlash scripts.
 
 =cut
 
-our $VERSION     = "3.3b1";
+our $VERSION     = "3.3b2";
 our @ISA         = qw(Exporter);
 our @EXPORT      = qw(
   $VERSION
diff --git a/README.md b/README.md
index 68325f1..f723728 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 <img align="right" src="docs/phyloFlash_logo.png" width="200" alt="phyloFlash logo"/>
 
-# phyloFlash v3.3 beta 1
+# phyloFlash v3.3b2
 
 [![GitHub (pre-)release](https://img.shields.io/github/release/HRGV/phyloflash/all.svg?label=Latest%20Version)]()
 [![Bioconda](https://img.shields.io/conda/vn/Bioconda/phyloFlash.svg)](https://bioconda.github.io/recipes/phyloflash/README.html)
@@ -42,11 +42,11 @@ If you clone the repository directly off GitHub you might end up with a version
 
 ```bash
 # Download latest release
-wget https://github.com/HRGV/phyloFlash/archive/pf3.3b1.tar.gz
-tar -xzf pf3.3b1.tar.gz
+wget https://github.com/HRGV/phyloFlash/archive/pf3.3b2.tar.gz
+tar -xzf pf3.3b2.tar.gz
 
 # Check for dependencies and install them if necessary
-cd phyloFlash-pf3.3b1
+cd phyloFlash-pf3.3b2
 ./phyloFlash.pl -check_env
 ```
 
@@ -113,6 +113,9 @@ For further information **please refer to the [Manual](https://hrgv.github.io/ph
 
 ## Versions and changes
 
+* v3.3 beta 2
+  * New options to graphical comparison scripts, and other small bug fixes
+  * Fix bug due to change in SILVA project file naming convention with SILVA 138 onwards
 * v3.3 beta 1
   * Add support for using SortMeRNA instead of BBmap for initial mapping step
   * Changes to how mapping data are hashed; process SAM file of initial mapping to fix known bugs with bitflag and read name reporting in BBmap and SortMeRNA
diff --git a/docs/index.md b/docs/index.md
index 27d95d6..12c4ec7 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -46,11 +46,11 @@ If you clone the repository directly off GitHub you might end up with a version
 
 ```bash
 # Download latest release
-wget https://github.com/HRGV/phyloFlash/archive/pf3.3b1.tar.gz
-tar -xzf pf3.3b1.tar.gz
+wget https://github.com/HRGV/phyloFlash/archive/pf3.3b2.tar.gz
+tar -xzf pf3.3b2.tar.gz
 
 # Check for dependencies and install them if necessary
-cd phyloFlash-pf3.3b1
+cd phyloFlash-pf3.3b2
 ./phyloFlash.pl -check_env
 ```
 
diff --git a/docs/install.md b/docs/install.md
index efc4710..b8eccd2 100644
--- a/docs/install.md
+++ b/docs/install.md
@@ -52,8 +52,8 @@ If you clone the repository directly off GitHub you might end up with a version
 
 ```bash
 # Download latest release
-wget https://github.com/HRGV/phyloFlash/archive/pf3.3b1.tar.gz
-tar -xzf pf3.3b1.tar.gz
+wget https://github.com/HRGV/phyloFlash/archive/pf3.3b2.tar.gz
+tar -xzf pf3.3b2.tar.gz
 ```
 
 Alternatively clone the latest development version with Git: