Reformatted README.md

Author: icwells

README.md

@@ -10,16 +10,14 @@
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     GNU General Public License for more details.
 
-
-##############################################################################
 # AlignmentProcessor1.1 Package
 
-#	Dependencies:	
-			Python 3
-			Python 3 version of Biopython
-			PAML (if using CodeML)
-			PhyML (if using CodeML)
-##############################################################################
+# Dependencies:	
+	Python 3
+	Python 3 version of Biopython
+	PAML (if using CodeML)
+	PhyML (if using CodeML)
+
 
 AlignmentProcessor is a pipeline meant to quickly convert a multi-fasta 
 alignment file into a format that can be read by KaKs_Calculator or PAML and 
@@ -31,15 +29,15 @@ based off of its sequences.
 You can run the AlignmentProcessor wrapper which will call all of the python 
 scripts in sequence, or you may call each script individually.
 
-### Installation
+# Installation
 
-# GitHub
+### GitHub
 AlignmentProcessor is freely available on GitHub and can either be downloaded directly from the site,
 can cloned using the following command:
 
 	git clone https://github.com/WilsonSayresLab/AlignmentProcessor.git
 
-# Installing Biopython
+### Installing Biopython
 Since Biopython offers the fastest and easiest ways to deal with alignments
 in a python script, it is used in several of the scripts in this package.
 The easiest way to install Biopython is to download a Python 3 version 
@@ -52,25 +50,25 @@ a terminal and Anaconda will install Biopython for you:
 
 	conda install -c https://conda.anaconda.org/anaconda biopython
 
-# KaKs_Calculator
+### KaKs_Calculator
 AlignmentProcessor0.21 is packaged with KaKs_Calculator2.0 binaries for Linux
 and Windows, and a KaKs_Calculator1.2 binary for Mac (there is no 2.0 binary
 available for OSX). Before using, copy or move the appropriate binary for your
 system into the AlignmentProcessor bin which contains the python scripts.
 
-# PAML
+### PAML
 If you plan to use CodeML, you must first download PAML 
 (http://abacus.gene.ucl.ac.uk/software/paml.html) and move the folder into the
 AlignmentProcessor directory. Make sure that it is titled "paml".
 
-# PhyML
+### PhyML
 If you plan to use CodeML, you must also download PhyML 
 (http://www.atgc-montpellier.fr/phyml/binaries.php). Similar to PAML, you must
 move the folder into the AlignmentProcessor directory and change the name of
 both the folder and the binary for your operating system to "PhyML".
 
-### Quick Start
+# Quick Start
 
 	python AlignmentProcessor.py --axt/phylip --kaks/codeml -r <reference species> -i <input fasta file> -o <path to output directory> 
 
-# Please see AlignmentPRocessorReadMe.pdf for specific options and instructions.
+### Please see AlignmentProcessorReadMe.pdf for specific options and instructions.