Mussagl Manual: Docs 1.0 updates (part two)

 * Updated Mac OS X install instruction. (ticket #168)
 * Documented why sub-analysis exists (ticket: #214)
 * Spelling err fix.
 * Hid changelog / major updates sections for future use. (ticket: #162)

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index ed4642d9dccc273d2d3df9ea9d1f7b1bad2e0477..df5426f561d53b5469b21289cb9916d09c99e0cd 100644 (file)
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -39,17 +39,16 @@ Documentation for Mussagl v1.0
 Status
 ======
 
-Major New Features
-------------------
-
- * Build 381
-   * Analysis "Save As" feature
+..
 
-Change Log
-----------
-
-.. INSERT CHANGE LOG HERE
-.. END INSERT CHANGE LOG
+  Major New Features
+  ------------------
+  
+  Change Log
+  ----------
+  
+  .. INSERT CHANGE LOG HERE
+  .. END INSERT CHANGE LOG
 
 Features to be Implemented
 --------------------------
@@ -80,7 +79,7 @@ Short History of Mussa
 Mussa Python/PMW Prototype
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-First Python/PMW based protoype.
+First Python/PMW based prototype.
 
 Mussa C++/FLTK
 ~~~~~~~~~~~~~~
@@ -128,11 +127,11 @@ Install
 
 Mac OS X
 ~~~~~~~~
-Once you have downloaded the .dmg file, double click on it and follow
-the install instructions. 
-
-FIXME: Mention how to launch the program.
 
+ * Download .dmg file.
+ * Double click on .dmg file.
+ * Drag Mussa icon to your /Applications folder.
+ * Double Click on Mussa icon to open program.
 
 Windows XP
 ~~~~~~~~~~
@@ -704,6 +703,10 @@ You should see the alignment at the base-pair level as shown below.
 Sub-analysis
 ------------
 
+Sub-analysis was created to allow you to analyze a sub-region using
+different parameters. This may allow you to find matches which may not
+have shown up with your initial settings.
+
 To run a sub-analysis **highlight** a section of sequence and *right
 click* on it and select **Add to subanalysis**. To the same for the
 sequences shown in orange in the screenshot below. Note that you **are