README version 1.0

Date: 30-Oct-2013
Author: Igor Filipovic 
Contact: filipovic.igor@gmail.com
Software: ddsilico v0.1

Publication: Genome-wide SNPs lead to strong signals of geographic structure 
and relatedness patterns in the major arbovirus vector, Aedes aegypti.
BMC Biology (submitted)

Description: This program performs in silico genome (or DNA sequence) 
digestion and counts the number of potential ddRAD loci.

Files included: 
 - ddsilico.exe (windows executable)
 - ddsilico (linux executable)
 - pstinger.fa (Stinger GFP transformation vector, complete sequence [GenBank: AF242364.2])
 - readme.txt

Installation:  Extract appropriate executable into a working directory.

Basic operation:  Once the program is started, you can change the default parameters: 
working directory, name of input file, name of comma separated output file,
fragment length bin size (in base pairs), maximum fragment length bin (in base pairs),
number of enzymes,  enzyme names, recognition site sequence and cut site position (offset
in base pairs on the 5' strand).

Output: Program generates a comma separated file that contains:
 - Categories (bin sizes in base pairs)
 - Same overhang (number of fragments in each bin which are generated by the same enzyme)
 - Different overhang (number of fragments in each bin which are generated by different
enzymes)
 - Sum of same overhang segments (sum of fragment lengths in each bin which are generated
by the same enzyme)
 - Sum of different overhang segments (sum of fragment lengths in each bin which are 
generated by different enzymes)
 - Sum of all segments (sum of all fragment lengths in each bin).