readme stuff

Author: MarkusRainerSchmidt

README.md

@@ -1,34 +1,38 @@
 
-## Getting started
+## Getting Started
 
 There are three options to get MA running:
-1. The installer
-2. Cloning & Compiling
-3. using pip (coming soon)
 
-### The installer
+#### 1. The Installer
 
-The installer is available on the It-Be homepage: 
+An installer is available on the It-Be homepage: 
 
 http://itbe.hanyang.ac.kr/research-articles/alignment/
 
-The installer is for 64bit **Windows** only.
+Note: The installer is currently the only way to obtain the GUI version of MA.
 
-
-### Cloning & Compiling
+#### 2. Cloning & Compiling
 This software uses boost 1.65.
 
-After downloading, set $(BOOST_ROOT) then execute following commands:
+After installing boost, set $(BOOST_ROOT) and execute following commands:
 
     git clone https://github.com/ItBeLab/ma
     cd ma
     make
     ./ma -h
 
-### Pip
+#### 3. Pip
 
 coming soon!
 
+### Aligning
+
+@todo
+
+### Generating Reference Indices
+
+@todo
+
 ## Introduction
 
 @todo
@@ -39,4 +43,5 @@ MA is unpublished so far.
 
 ## The It-Be Lab
 
-The homepage of the **Information Technology – Bio Engineering** Lab at Hanyang University can be found here http://itbe.hanyang.ac.kr/.
+The homepage of the **Information Technology – Bio Engineering** Lab 
+at Hanyang University can be found here http://itbe.hanyang.ac.kr/.