RAD SNP genotype tools
Tool Repository


SOFTWARE NAME: RAD SNP genotype tools VERSION: beta 1.0, November 2013 AUTHORS: Guangtu Gao and Michael R. Miller BRIEF DESCRIPTION: This package contains several Perl scripts to implement a pipeline of calling genotypes from RAD sequencing. The scripts were developed based on the original scripts by Michael Miller for a similar paper (see Reference). PUBLICATION: Yniv Palti, Guangtu Gao, Michael R. Miller, Roger L. Vallejo, Paul A. Wheeler, Edwige Quillet, Jianbo Yao, Gary H. Thorgaard, Mohamed Salem, Caird E. Rexroad III "A resource of single-nucleotide polymorphisms for rainbow trout generated by RAD sequencing of doubled haploids". Submitted to Molecular Ecology Resources. PLATFORM and ENVIRONMENT REQUIREMENT: Dos, Windows 3.x, 9x, 2000, NT, XP, Linux, Unix, and any other platform where perl 5.8.0 or above DOWNLOAD: INSTALLATION: * 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. USAGE: 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) 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. 4) See the README file for how to run each of the scripts, including the input and output of the files. WEB SITE: 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. REFERENCE: Miller MR, Brunelli JP, Wheeler PA, et al. (2012) A conserved haplotype controls parallel adaptation in geographically distant salmonid populations. Molecular Ecology 21, 237-249. CONTACT: For any question using the software or suggestions to improve, contact: guangtu.gaoars.usda.gov.
File NameSizeDate/Time Accessed
HOWTO.txt2.02 KB2022-09-27 11:22:31


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