Merge pull request #18 from bewt85/bt5-clean-up-readme

Reformat README

README.md

@@ -1,40 +1,36 @@
 [![Build Status](https://travis-ci.org/sanger-pathogens/snp_sites.png?branch=master)](https://travis-ci.org/sanger-pathogens/snp_sites)
-SNP Sites
-=====
+# SNP Sites
 This program finds snp sites from a multi fasta alignment file.
 
-
+```
 Usage: snp-sites [-mvph] [-o output_filename] <file>
 This program finds snp sites from a multi fasta alignment file.
- -m		output a multi fasta alignment file (default)
- -v		output a VCF file
- -p		output a phylip file
- -o		specify an output filename
- -h		this help message
+ -m		    output a multi fasta alignment file (default)
+ -v		    output a VCF file
+ -p		    output a phylip file
+ -o		    specify an output filename
+ -h		    this help message
  <file>		input alignment file which can optionally be gzipped
-
+```
 
 This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in the following formats:
 
-a multi fasta alignment,
-VCF, 
-relaxed phylip format.
+- a multi fasta alignment,
+- VCF, 
+- relaxed phylip format.
 
-Example usage:
+### Example usage
 
+```
 snp-sites my_alignment.aln
-
 snp-sites my_gzipped_alignment.aln.gz
+```
 
-
-Multi Fasta Alignment
-=====
+### Multi Fasta Alignment
 Similar to the input file but just containing the SNP sites.
 
-VCF
-=====
+### VCF
 This contains the position of each SNP in the reference sequence, and the occurrence in each other sample. Can be loaded into Artemis for visualisation.
 
-Relaxed Phylip format
-=====
+### Relaxed Phylip format
 All the SNP sites in a format for RAxML and other tree building applications.