diff --git a/README.md b/README.md
index c4b0bc198b1929408d472536bb5c06c0d3bb069e..3b16480f63d54616969919eb4b8da67d6b350ed8 100644
--- a/README.md
+++ b/README.md
@@ -6,25 +6,17 @@ evel repository for easier use by experimental chemists.
 
 ## How do I get set up? ##
 
-* Summary of set up
-* Configuration
-* Dependencies
-* Database configuration
-* How to run tests
-* Deployment instructions
-
 ### Required modules ###
 
 The other modules produced by Mark Driver required for this work to function are:
 
     * xmlvalidator [bitbucket](https://bitbucket.org/mdd31/xmlvalidator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/xmlvalidator)
-    * puresolventinformation [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
-    * resultsanalysis [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
-    * phasexmlparser [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
-    * phasexmlcreator [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
-    * resultsanalysis [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
-    * solventmapcreator [bitbucket](https://bitbucket.org/mdd31/) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/)
-    * ssip [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssip) 
+    * puresolventinformation [bitbucket](https://bitbucket.org/mdd31/puresolventinformation) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/puresolventinformation)
+    * resultsanalysis [bitbucket](https://bitbucket.org/mdd31/resultsanalysis) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/resultsanalysis)
+    * phasexmlparser [bitbucket](https://bitbucket.org/mdd31/phasexmlparser) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlparser)
+    * phasexmlcreator [bitbucket](https://bitbucket.org/mdd31/phasexmlcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlcreator)
+    * solventmapcreator [bitbucket](https://bitbucket.org/mdd31/solventmapcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/solventmapcreator)
+    * ssip (specifically phasetransfer module) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssip)
     
 ### Clone this repository ###
 
@@ -54,7 +46,7 @@ This creates and environment callled 'resultsanalysis' which can be loaded using
 
 Before installing this module please make sure that the required modules listed previously are installed in the current python environment. Before cloning the dependent repositories please change up a directory and follow install instructions to install in this environment.
 
-For the SSIP phasetransfer module please compile a jar with dependencies as detailed in the repository documentation.
+For the SSIP phasetransfer module please compile a jar with dependencies as detailed in the repository documentation (This requires version 6.0.0 or greater). A pre-compiled jar with dependencies may be available on the repository \_\_\_ page.
 
 ### Using pip to install module ###
 
@@ -75,25 +67,38 @@ The CLI has been implemented to enable operation in two modes:
 
 1) Run calculations from input XML.
 
-This uses the 
+This uses the calculate option of the CLI.
 
 2) Generate input XML for default solvents.
 
-This uses the 
+This uses the inpgen option of the CLI.
 
 See the help arguments for more information about the options.
 
 #### Example calculations ####
 
-The
+Please see the examples included in the bottom of the help statements for the inpgen and calculate modules.
+
+### Notes about file formats ###
+
+#### CSV file format for phase information ####
+
+The CSV file of phase information used by inpgen to create the phase calculator XML has the following specification.
+
+- The file is tab '\t' delimited, and fields are not quoted.
+- One solvent/phase entry per row.
+- First column contains the temperature.
+- Subsequent columns contain molecule name and molefraction for each molecule present in the solvent/phase.
+- Illustrative line is below:
 
+	TEMP	MOL_NAME1	MOL_FRAC1	MOL_NAME2	MOL_FRAC2	...
 
-The csv file of solvent information is in 
 
 Default solvent names for inclusion in the CSV file can be found by running:
 
-    python -m phasecalculator #ADD method- new subprocessor. 
+    python -m phasecalculator solventnames
 
+This lists the accepted names of components for use with the CLI. For more advanced usage please see the source code documentation.
 
 ### Documentation ###