diff --git a/CMakeLists.txt b/CMakeLists.txt
index 29bab350f118cacdf1eac78632f14c5a38e92242..da26e1e61e6866c4eee1d27de507db1edcf27e49 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -48,28 +48,28 @@ endif()
 
 if(ENABLE_HISTOGRAM)
   message(STATUS "Enabled: Histogram analysis.")
-  add_subdirectory(histogram)
+  add_subdirectory(analysis/histogram)
 else()
   message(STATUS "Disabled: Histogram analysis.")
 endif()
 
 if(ENABLE_AUTOCORRELATION)
   message(STATUS "Enabled: Autocorrelation analysis.")
-  add_subdirectory(autocorrelation)
+  add_subdirectory(analysis/autocorrelation)
 else()
   message(STATUS "Disabled: Autocorrelation analysis.")
 endif()
 
 if(ENABLE_PARALLEL3D)
   message(STATUS "Enabled: Parallel3D miniapp.")
-  add_subdirectory(parallel3d)
+  add_subdirectory(miniapps/parallel3d)
 else()
   message(STATUS "Disabled: Parallel3D miniapp.")
 endif()
 
 if(ENABLE_OSCILLATORS)
   message(STATUS "Enabled: Oscillators miniapp.")
-  add_subdirectory(oscillators)
+  add_subdirectory(miniapps/oscillators)
 else()
   message(STATUS "Disabled: Histogram miniapp.")
 endif()
diff --git a/autocorrelation/AutocorrelationAnalysisAdaptor.cxx b/analysis/autocorrelation/AutocorrelationAnalysisAdaptor.cxx
similarity index 100%
rename from autocorrelation/AutocorrelationAnalysisAdaptor.cxx
rename to analysis/autocorrelation/AutocorrelationAnalysisAdaptor.cxx
diff --git a/autocorrelation/AutocorrelationAnalysisAdaptor.h b/analysis/autocorrelation/AutocorrelationAnalysisAdaptor.h
similarity index 100%
rename from autocorrelation/AutocorrelationAnalysisAdaptor.h
rename to analysis/autocorrelation/AutocorrelationAnalysisAdaptor.h
diff --git a/autocorrelation/CMakeLists.txt b/analysis/autocorrelation/CMakeLists.txt
similarity index 100%
rename from autocorrelation/CMakeLists.txt
rename to analysis/autocorrelation/CMakeLists.txt
diff --git a/autocorrelation/analysis.cpp b/analysis/autocorrelation/analysis.cpp
similarity index 100%
rename from autocorrelation/analysis.cpp
rename to analysis/autocorrelation/analysis.cpp
diff --git a/autocorrelation/analysis.h b/analysis/autocorrelation/analysis.h
similarity index 100%
rename from autocorrelation/analysis.h
rename to analysis/autocorrelation/analysis.h
diff --git a/histogram/CMakeLists.txt b/analysis/histogram/CMakeLists.txt
similarity index 100%
rename from histogram/CMakeLists.txt
rename to analysis/histogram/CMakeLists.txt
diff --git a/histogram/HistogramAnalysisAdaptor.cxx b/analysis/histogram/HistogramAnalysisAdaptor.cxx
similarity index 100%
rename from histogram/HistogramAnalysisAdaptor.cxx
rename to analysis/histogram/HistogramAnalysisAdaptor.cxx
diff --git a/histogram/HistogramAnalysisAdaptor.h b/analysis/histogram/HistogramAnalysisAdaptor.h
similarity index 100%
rename from histogram/HistogramAnalysisAdaptor.h
rename to analysis/histogram/HistogramAnalysisAdaptor.h
diff --git a/histogram/histogram.cpp b/analysis/histogram/histogram.cpp
similarity index 100%
rename from histogram/histogram.cpp
rename to analysis/histogram/histogram.cpp
diff --git a/histogram/histogram.h b/analysis/histogram/histogram.h
similarity index 100%
rename from histogram/histogram.h
rename to analysis/histogram/histogram.h
diff --git a/histogram/vtk_histogram.cxx b/analysis/histogram/vtk_histogram.cxx
similarity index 100%
rename from histogram/vtk_histogram.cxx
rename to analysis/histogram/vtk_histogram.cxx
diff --git a/histogram/vtk_histogram.h b/analysis/histogram/vtk_histogram.h
similarity index 100%
rename from histogram/vtk_histogram.h
rename to analysis/histogram/vtk_histogram.h
diff --git a/oscillators/CMakeLists.txt b/miniapps/oscillators/CMakeLists.txt
similarity index 100%
rename from oscillators/CMakeLists.txt
rename to miniapps/oscillators/CMakeLists.txt
diff --git a/oscillators/README.md b/miniapps/oscillators/README.md
similarity index 100%
rename from oscillators/README.md
rename to miniapps/oscillators/README.md
diff --git a/oscillators/bridge.cpp b/miniapps/oscillators/bridge.cpp
similarity index 100%
rename from oscillators/bridge.cpp
rename to miniapps/oscillators/bridge.cpp
diff --git a/oscillators/bridge.h b/miniapps/oscillators/bridge.h
similarity index 100%
rename from oscillators/bridge.h
rename to miniapps/oscillators/bridge.h
diff --git a/oscillators/dataadaptor.cpp b/miniapps/oscillators/dataadaptor.cpp
similarity index 100%
rename from oscillators/dataadaptor.cpp
rename to miniapps/oscillators/dataadaptor.cpp
diff --git a/oscillators/dataadaptor.h b/miniapps/oscillators/dataadaptor.h
similarity index 100%
rename from oscillators/dataadaptor.h
rename to miniapps/oscillators/dataadaptor.h
diff --git a/oscillators/include/format.h b/miniapps/oscillators/include/format.h
similarity index 100%
rename from oscillators/include/format.h
rename to miniapps/oscillators/include/format.h
diff --git a/oscillators/include/opts/opts.h b/miniapps/oscillators/include/opts/opts.h
similarity index 100%
rename from oscillators/include/opts/opts.h
rename to miniapps/oscillators/include/opts/opts.h
diff --git a/oscillators/oscillator.cpp b/miniapps/oscillators/oscillator.cpp
similarity index 100%
rename from oscillators/oscillator.cpp
rename to miniapps/oscillators/oscillator.cpp
diff --git a/oscillators/oscillator.h b/miniapps/oscillators/oscillator.h
similarity index 100%
rename from oscillators/oscillator.h
rename to miniapps/oscillators/oscillator.h
diff --git a/oscillators/sample.osc b/miniapps/oscillators/sample.osc
similarity index 100%
rename from oscillators/sample.osc
rename to miniapps/oscillators/sample.osc
diff --git a/oscillators/src/format.cc b/miniapps/oscillators/src/format.cc
similarity index 100%
rename from oscillators/src/format.cc
rename to miniapps/oscillators/src/format.cc
diff --git a/parallel3d/Bridge.cxx b/miniapps/parallel3d/Bridge.cxx
similarity index 100%
rename from parallel3d/Bridge.cxx
rename to miniapps/parallel3d/Bridge.cxx
diff --git a/parallel3d/Bridge.h b/miniapps/parallel3d/Bridge.h
similarity index 100%
rename from parallel3d/Bridge.h
rename to miniapps/parallel3d/Bridge.h
diff --git a/parallel3d/CMakeLists.txt b/miniapps/parallel3d/CMakeLists.txt
similarity index 100%
rename from parallel3d/CMakeLists.txt
rename to miniapps/parallel3d/CMakeLists.txt
diff --git a/parallel3d/DataAdaptor.cxx b/miniapps/parallel3d/DataAdaptor.cxx
similarity index 100%
rename from parallel3d/DataAdaptor.cxx
rename to miniapps/parallel3d/DataAdaptor.cxx
diff --git a/parallel3d/DataAdaptor.h b/miniapps/parallel3d/DataAdaptor.h
similarity index 100%
rename from parallel3d/DataAdaptor.h
rename to miniapps/parallel3d/DataAdaptor.h
diff --git a/parallel3d/parallel_3D.c b/miniapps/parallel3d/parallel_3D.c
similarity index 100%
rename from parallel3d/parallel_3D.c
rename to miniapps/parallel3d/parallel_3D.c