1. tss101
  2. optiCall

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-INSTALLATION
+==== REQUIREMENTS ====
 
+opticall includes all the libraries it needs, and requires nothing beyond the C++ standard. It compiles using g++ on unix/mac based systems.
 
+==== INSTALLATION ====
 
-USAGE
+You can download the latest release of opticall from:
+
+https://bitbucket.org/tss101/opticall/downloads
+
+download the most recent compressed file in the format you're most comfortable with. In the case of a .gz download, uncompress the file by running:
+
+tar xvzf <filename>
+
+which creates a folder of the same name as filename. cd into the optical folder:
+
+cd <foldername>/opticall
+
+then compile the opticall code by running the make command:
+
+make
+
+after which the opticall executable will appear, and you've installed opticall
+
+==== USAGE ====
 
 opticall [options] [-in INPUT_FILE] [-out OUTPUT_FILE]
  
  
-DESCRIPTION
+==== DESCRIPTION ====
 
 opticall reads in file of intensity data (currently Illumina normalized intensities) and clusters them considering both per-SNP and per-sample information, and provides genotype calls as output. The intensity input file is tab separated, with SNPs are rows, and samples as columns. So a line would be: 
 
 
 An example input intensity file is provided with the program for your information.
  
-OPTIONS
+==== OPTIONS ====
 
 -in FILE