A new computational pipeline to discover SNPs based on CAP3 alignments

  VERSION: beta 1.10, February 2009
  AUTHORS: Danielle Gorbach, Zhi-Liang Hu, and Max Rothschild

  This package is designed to predict the location of SNPs from clusters
  of ESTs produced by the program CAP3. For more details, please refer 
  to the documentation that is distributed together with the package.

  Gorbach, Danielle M., Zhi-Liang Hu, Zhi-Qiang Du and M. F. Rothschild (2009)
  "SNP discovery in Litopenaeus vannamei with a new computational pipeline".
  Animal Genetics, 40(1):106-109.

  Dos, Windows 3.x, 9x, 2000, NT, XP, Linux, Unix, and any other platform
  where perl 5.8.0 or above and required libraries are installed 


  * On Linux/Unix/Mac OS X platforms:
    1. Download and unpackage the program ('gunzip', 'tar -xf-'; or 'tar zxf');
    2. Change the first line in the program with proper path pointing to perl
       in your system;
    3. Make the program file excutable (e.g. on unix/Linux, do "chmod 755").
  * On Windows platforms:
  The steps are similar; except that you need to install ActivePerl to run it.
  Although you can make it a ".exe" file but it's recommanded to run on command
  line. You may need UnZip or RAR to uncompress the downloaded file.

  To run this program, follow these steps:
  1) Change the first line of this program to point to the correct path 
     for perl on your computer.
  2) Perl 5.8.0 or higher (ActivePerl for Windows machine) much be installed
     on your computer. 
  3) You must have a set of contigs that were obtained from CAP3 run of
     your raw sequences (the CAP3 alignment serves as your input file).
  4) Run this program on command line (For Windows, open the command prompt;
     For Mac OS or Linux, bring up the terminal window): change directory 
     to the location of this program.  Then type the name of the program and 
     hit "enter" to run.

  > script_name

  This program takes standard output (displaying consensus sequence
  alignments) from "cap3" as input.  No modification is needed.

  This program outputs results in two files:

  - One file (default name "find.snp.seq.txt") contains all consensus 
    sequences that are identified to contain at least one SNP. Each record
    is tab delimited:
    1. Name of the sequence
    2. Sequence itself

  - One file (default name "find.snp.sta.txt") contains all statistics
    that descibe each virtually identified SNP. The statistics are tab-
    delimited, one line for each SNP, include:
    1. SNP scores (minor allele frequency x the number of sequences
       containing the minor allele).
    2. The contig number (sequence name)
    3. SNP location (number of bases from left end of the seq.)
    4. Minor nucleotide (allele) frequencies
    5. Number of aligned sequences that contribute to the SNP scoring

  Check the SNPidentifier web site for recent changes and future updates:

  This is a trial version which we authorize for non-profit use and 
  distribution for evaluation. We are not responsible for possible 
  errors that may exist in the program. Any use of the package is free
  provided that the purpose of use is for evaluation, education and non-
  profit research. The authors appreciate feedbacks from users for further 
  improvement. Original codes are available upon request to the authors. 
  All other rights are reserved that include modification and recompilation
  of the programs.

  Gorbach DM, Hu ZL, Du ZQ, Rothschild MF. (2009).
  SNP discovery in Litopenaeus vannamei with a new computational pipeline.
  Anim Genet. Volume 40, Issue 1, pages 106-109.

  For any question using the software or suggestions to improve, contact: