diff --git a/CMakeLists.txt b/CMakeLists.txt
index 220eb69..79d3612 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -31,4 +31,4 @@ add_subdirectory (src/init init)
 add_subdirectory (src/seq_generator seq_generator)
 add_subdirectory (src/seq_scoring seq_scoring)
 add_subdirectory (src/refinement bamm)
-add_subdirectory (src/evaluation fdr)
+add_subdirectory (src/evaluation evaluation)
diff --git a/src/evaluation/CMakeLists.txt b/src/evaluation/CMakeLists.txt
index 368ad00..0b219ff 100644
--- a/src/evaluation/CMakeLists.txt
+++ b/src/evaluation/CMakeLists.txt
@@ -1,8 +1,9 @@
 file(GLOB SOURCES *.cpp *.h ../refinement/EM.* ../refinement/GibbsSampling.*)
+
 add_executable (FDR ${SOURCES})
 
 target_link_libraries (FDR LINK_PUBLIC init)
 target_link_libraries (FDR LINK_PUBLIC seq_scoring)
 target_link_libraries (FDR LINK_PUBLIC seq_generator)
 
-add_library (fdr ${SOURCES})
+add_library (evaluation ${SOURCES})
diff --git a/src/getopt_pp/CMakeLists.txt b/src/getopt_pp/CMakeLists.txt
index 449eb55..799d57d 100644
--- a/src/getopt_pp/CMakeLists.txt
+++ b/src/getopt_pp/CMakeLists.txt
@@ -1,2 +1,3 @@
 file(GLOB SOURCES *.cpp *.h)
+
 add_library (getopt_pp ${SOURCES})
\ No newline at end of file
diff --git a/src/init/CMakeLists.txt b/src/init/CMakeLists.txt
index eb15d69..c4adc17 100644
--- a/src/init/CMakeLists.txt
+++ b/src/init/CMakeLists.txt
@@ -1,4 +1,3 @@
 file(GLOB SOURCES *.cpp *.h)
-add_library (init ${SOURCES})
 
-target_include_directories (init PUBLIC ../sequences)
\ No newline at end of file
+add_library (init ${SOURCES})
diff --git a/src/refinement/CMakeLists.txt b/src/refinement/CMakeLists.txt
index e73b832..ed6871a 100644
--- a/src/refinement/CMakeLists.txt
+++ b/src/refinement/CMakeLists.txt
@@ -1,9 +1,10 @@
 file(GLOB SOURCES *.cpp *.h)
+
 add_executable (BaMMmotif ${SOURCES})
 
 target_link_libraries (BaMMmotif LINK_PUBLIC getopt_pp)
 target_link_libraries (BaMMmotif LINK_PUBLIC init)
-target_link_libraries (BaMMmotif LINK_PUBLIC fdr)
+target_link_libraries (BaMMmotif LINK_PUBLIC evaluation)
 target_link_libraries (BaMMmotif LINK_PUBLIC seq_scoring)
 target_link_libraries (BaMMmotif LINK_PUBLIC seq_generator)
 
diff --git a/src/seq_scoring/CMakeLists.txt b/src/seq_scoring/CMakeLists.txt
index 495565a..620e7f1 100644
--- a/src/seq_scoring/CMakeLists.txt
+++ b/src/seq_scoring/CMakeLists.txt
@@ -1,4 +1,5 @@
 file(GLOB SOURCES *.cpp *.h ../seq_generator/SeqGenerator.*)
+
 add_executable (BaMMScan ${SOURCES})
 
 target_link_libraries (BaMMScan LINK_PUBLIC init)