How to Acquire PolyPhred

PolyPhred is available for these platforms:
  • Linux (x86 and x86-64)
  • Mac OS X (PowerPC and x86)
  • Cygwin
  • Solaris (x86 and SPARC)
  • SGI IRIX
  • Compaq Tru64 Alpha (formerly DEC OSF/1)
  • HP-UX (PA-RISC)
  • AIX 5 (PowerPC)

License agreement

Copyright 2002 University of Washington.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to a non-exclusive, nontransferable, perpetual license to copy, modify, and perform the Software for non-profit academic research purposes. Distribution of the Software is not permitted. Use of the Software is restricted to non-commercial research purposes.

For commercial uses, please contact license@uw.edu

The above copyright notice and this permission notice shall be included in all copies, modifications or substantial portions of the Software.

If utilization of the Software results in outcomes that will be published, you agree to cite the appropriate article.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Academic and Non-Profit Institutions

Polyphred is freely available to researchers at academic and non-profit institutions. To acquire Polyphred, please 1) read the license agreement, and 2) click on the appropriate download link.

Commercial Businesses

Commercial businesses wanting to acquire Polyphred are required to contact license@uw.edu and to purchase a commercial license agreement.

Downloading PolyPhred

To download PolyPhred, click on one of the links below:

PolyPhred 6.18

PolyPhred 6.15 Beta

PolyPhred 6.02 Beta

PolyPhred 5.04

Instructions

If you need to download PolyPhred for more than one operating system, and you got an "authorization failure" message after the first download, please 'reload' this page and try again.

The downloaded file has been 'tarred' and compressed with gzip. It contains:
   polyphredthe executable PolyPhred program *
   sudophreda tool for generating fake chromat, PHD and POLY files from sequence data in FASTA format.
   polygena tool for generating phd and poly files ABI files containing KB base-caller data - an alternative to Phred.
   polyphred.html   the PolyPhred documentation in html format.
   phredPhrapa script written in Perl that runs the programs phred and phrap

To unpack the file, move it to an empty directory. Go to that directory and run these commands:

  tar xzf [filename]
where [filename] is the name of the downloaded file. For example: 
  tar xzf polyphred_linux.tar.gz

Instructions for installing and setting up PolyPhred are included in the documentation file, polyphred.html.

Example data sets for those who are using PolyPhred for the first time

We suggest that new PolyPhred users also download our example package, which contains a sample data set and a brief tutorial on how to analyze the data with PolyPhred. You do not need a password to download these files.

Download for all platforms (tar/gzip)

Unpack by running: gunzip -c polyphred-snp-example.tar.gz | tar xvf -

These commands will extract the archive into a directory named polyphred-snp-example, which contains the sample data and a README file.

This data set contains an example of heterozygous indel in one of the reads.

Download for all platforms (except DEC-Alpha 4)

After downloading this file, unpack it with the following commands: 

 gunzip csft2.tar.gz
 tar xf csft2.tar

Return to the main PolyPhred page