SOFTWARE NAME: SNPidentifier
      VERSION: beta 1.00, December 2007
      AUTHORS: Danielle Bowen, Zhi-Liang Hu, and Max Rothschild

BRIEF DESCRIPTION:
  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.

PUBLICATION:
  Bowen, Danielle M., Zhi-Liang Hu, Zhi-Qiang Du and M. F. Rothschild (2008)
  "SNP discovery in Litopenaeus vannamei with a new computational pipeline".
  Animal Genetics, (Accepted for publication, details to be updated)

PLATFORM:
  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.

DOWNLOAD:
  http://www.animalgenome.org/bioinfo/tools/share/SNPidentifier/script.tar.gz

INSTALLATION:
  Download and unpackage the program (gunzip; tar -xf-). Identify proper
  path to perl -- that's all you need to set it up.

USAGE:
  Run on command line:
  > script_name input_file_name

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

DATA OUTPUT:
  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

AUTHOR'S CLAIM:
  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.

CONTACT:
  For any question using the software or suggestions to improve, contact:
  dmbowen@iastate.edu
  zhu@iastate.edu
  mfrothsc@iastate.edu