diff --git a/README.md b/README.md
index 5ea70b4f4015593e6b2b86cde380bc07e2f59cf9..9485def8fd4b1b3f00d323f22118c3fae8d86323 100644
--- a/README.md
+++ b/README.md
@@ -21,10 +21,11 @@ list of PDB files.
 Be sure to check if the following packages are correctly installed with
 your python installation or virtual environment.
 
-- **pip** (>= 9.0)
-- **setuptools** (>= 18.0)
+- **pip** (>= 18.0)
+- **git** (>= 2.0)
 - **cns-solve** (1.21)
-- **pbxplore** (>= 1.3.8)
+- **ccpnmr analysis** (optional)
+- **ccpn data model** (optional)
 
 Then the easiest solution is to call the **pip** command below :
 
@@ -33,7 +34,8 @@ Then the easiest solution is to call the **pip** command below :
 For more information about installation and usage, please refer to the
 [ARIAEC documentation](http://bis-aria.pages.pasteur.fr/ariaec)
 
-**ARIA contains patches for CNS-solve which needs to be compiled after the installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
+**ARIA contains patches for CNS-solve which needs to be compiled after the
+installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
 
     
 ## Contributing
diff --git a/docs/contents.rst b/docs/contents.rst
index 52d2f28f5d8cde74bff524accae7a1052b7c8da0..4e7e833e11b4517781612af047571e69f1908b19 100644
--- a/docs/contents.rst
+++ b/docs/contents.rst
@@ -8,20 +8,11 @@
    usage
    contributing
 
-.. toctree::
-   :maxdepth: 4
-   :caption: API
-
-   Core package <api/aria.core>
-   Conbox package <api/aria.conbox>
-
 .. toctree::
    :maxdepth: 2
    :caption: Tutorial
 
-   tutorial/setup
-   tutorial/run
-   tutorial/analysis
+   tutorial
 
 .. toctree::
    :maxdepth: 2
@@ -29,3 +20,11 @@
 
    examples/bpt1/bpt1
    examples/malecoli/malecoli
+
+.. toctree::
+   :maxdepth: 4
+   :caption: API
+
+   Core package <api/aria.core>
+   Conbox package <api/aria.conbox>
+
diff --git a/docs/installation.rst b/docs/installation.rst
index fc0c882b87844531d97f361975c3b9e692d92bc7..6512966d94aea58c010ce90deec656902c63adaa 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -203,8 +203,8 @@ version 1.2 :
 2. Edit the file ``cns_solve_env`` in the directory ``cns_solve_1.1`` to define
 the location of the CNSsolve directory.
 
-3. Go to directory ``cns_solve_1.1`` and type ``make install``. This should start
-the compilation process.
+3. Go to the directory ``cns_solve_1.1`` and type ``make install``. This should
+start the compilation process.
 
 
 .. Footnotes
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f4b5d31d6eac2a5f0d4cdd421ac8dec5897c7e4e
--- /dev/null
+++ b/docs/tutorial.rst
@@ -0,0 +1,29 @@
+========
+Tutorial
+========
+
+Project preparation
+===================
+
+The ``ariaec`` Command Line Interface (CLI) is the main tool for
+converting and analyze contact map information. The main command of this
+interface is ``ariaec setup`` which create an ARIA project XML file. Then we can
+follow the usual steps for an ARIA project.
+
+Configuration file
+------------------
+
+All the parameters for ``ariaec`` commands are encapsulated on a configuration file in INI format
+
+
+Project template
+----------------
+
+
+Setup
+-----
+
+
+Running ARIA
+============
+
diff --git a/docs/usage.rst b/docs/usage.rst
index 1ae0e6f2df3f244dc34ad96d44e688b661a07964..6f1c402ee803bff2f9a886a43dd848220d98d9da 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -17,7 +17,7 @@ ARIAEC
 
 .. code-block:: shell
 
-    ariaec [-h]  COMMAND
+    ariaec COMMAND [OPTIONS] ARGS
 
 
 **Commands**
@@ -56,14 +56,14 @@ ARIAEC
 
 .. rst-class:: table-hover
 
+.. list-table::
+    :header-rows: 1
+    :widths: 25 60
 
-+--------------------------------------------------------+-----------------------------------------------------+
-|  Name                                                  | Description                                         |
-+========================================================+=====================================================+
-| ``-h``, ``--help``                                     | show help message and exit                          |
-+--------------------------------------------------------+-----------------------------------------------------+
-
-
+    *   - Name
+        - Short Description
+    *   - ``-h``, ``--help``
+        - show help message and exit
 
 Setup
 +++++
@@ -71,21 +71,23 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj
 
 .. code-block:: shell
 
-    ariaec setup SEQFILE INFILE [INFILE ...] -o OUTPUT_DIRECTORY [-c CONF_FILE] -t INTYPE [INTYPE ...]
+    ariaec setup [OPTIONS] SEQFILE INFILE [INFILE ...] -o OUTPUT_DIRECTORY -t INTYPE [INTYPE ...]
 
 
 **Arguments**
 
 .. rst-class:: table-hover
 
+.. list-table::
+    :header-rows: 1
+    :widths: 25 60
 
-+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-|  Name                   | Short description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
-| ``seq``                 | Sequence file [``FASTA``]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
-+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``infile [infile ...]`` | Contact or pdb file(s) used to build aria distance restraints                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
-+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+    *   - Name
+        - Short Description
+    *   - ``seq``
+        - Sequence file [``FASTA``]
+    *   - ``infile [infile ...]``
+        - Contact or pdb file(s) used to build aria distance restraints
 
 .. _ConKit: http://www.conkit.org/en/latest/
 
@@ -95,40 +97,42 @@ Translate contact maps as distance restraints and initialize a new ARIA XML proj
 
 .. rst-class:: table-hover
 
+.. list-table::
+    :header-rows: 1
+    :widths: 25 60
 
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-|  Name                                                  | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
-+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
-| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-c CONF_FILE``, ``--conf CONF_FILE``                 | configuration file (default: None)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``--nolog``                                            | Don't generate log files (default: False)                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-d``, ``--debug``                                    | Increase output verbosity (default: False)                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-t intype [intype ...]``                             | Contact Map file format:sup:`*`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-d DISTFILE``, ``--distfile DISTFILE``               | Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints                                                                                                                                                                                                                                                                                                                                                                  |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-s SSPRED``, ``--ssfile SSPRED``                     | Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT``      | ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call                                                                                                                                                                                                                                                                                                                                                                                                                    |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-r SEQRANGE``, ``--range SEQRANGE``                  | Index range if we don't want tu use the whole sequence and map                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-n REF``, ``--native REF``                           | Native pdb. Allow TP/FP detection                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``--hb HB``                                            | H-bonds contact file (eg: metapsicov.hb)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``--ssidx``                                            | Use secondary structure index                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``--no-filter``                                        | Do not filter contact map                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``--extract-all``                                      | Extract data or all data and parameters if an ARIA project is defined with ``-p`` option                                                                                                                                                                                                                                                                                                                                                                                                                                |
-+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib`` |
-+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+    *   - Name
+        - Short Description
+    *   - ``-h``, ``--help``
+        - show help message and exit
+    *   - ``-d``, ``--debug``
+        - Increase output verbosity (default: False)
+    *   - ``--nolog``
+        - Don't generate log files (default: False)
+    *   - ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY``
+        - Output directory (default: None)
+    *   - ``-c CONF_FILE``, ``--conf CONF_FILE``
+        - configuration file (default: None)
+    *   - ``-t intype [intype ...]``
+        - Contact Map file format:sup:`*`
+    *   - ``-d DISTFILE``, ``--distfile DISTFILE``
+        - Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints
+    *   - ``-s SSPRED``, ``--ssfile SSPRED``
+        - Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus
+    *   - ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT``
+        - ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call
+    *   - ``-r SEQRANGE``, ``--range SEQRANGE``
+        - Index range if we don't want tu use the whole sequence and map
+    *   - ``-n REF``, ``--native REF``
+        - Native pdb. Allow TP/FP detection
+    *   - ``--hb HB``
+        - H-bonds contact file (eg: metapsicov.hb)
+    *   - ``--no-filter``
+        - Do not filter contact map
+    *   - ``--extract-all``
+        - Extract data or all data and parameters if an ARIA project is defined with ``-p`` option
+    *   - ``--ssidx``
+        - :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib``
 
 
 Bbconv
@@ -138,7 +142,7 @@ Translate BBcontacts as distance restraints which can be used during
 
 .. code-block:: shell
 
-    ariaec bbconv [-h] contactfile sspred seq [msa] -t contactype
+    ariaec bbconv [OPTIONS] CONTACTFILE SSPRED SEQ [MSA] -t CONTACTYPE
 
 
 **Arguments**