diff --git a/.gitmodules b/.gitmodules
index 110a5ff..868f845 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -19,3 +19,6 @@
 [submodule "ngsDist"]
 	path = ngsDist
 	url = https://github.com/fgvieira/ngsDist.git
+[submodule "ngsF-HMM"]
+	path = ngsF-HMM
+	url = https://github.com/fgvieira/ngsF-HMM.git
diff --git a/CHANGELOG b/CHANGELOG
index 52b0d59..c741d5d 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,8 @@
+
+1.0.1 / 20-05-2016
+==================
+  * Added ngsF-HMM as a sub-repository
+
 1.0.0 / 23-03-2016
 ==================
   * Added support for ANGSD's new SAF format
diff --git a/Makefile b/Makefile
index 4b9428c..b3ec1aa 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 
 EXT = htslib angsd
-TOOLS = ngsSim ngsPopGen ngsUtils ngsDist ngsF
+TOOLS = ngsSim ngsPopGen ngsUtils ngsDist ngsF ngsF-HMM
 
 
 all: $(EXT) $(TOOLS)
diff --git a/ngsF-HMM b/ngsF-HMM
new file mode 160000
index 0000000..9fa7675
--- /dev/null
+++ b/ngsF-HMM
@@ -0,0 +1 @@
+Subproject commit 9fa7675a3deb10dcc7a0966695558e47702a426c