How to Acquire PolyPhred 6.11 Beta

PolyPhred 6.11 Beta is now available – see PolyPhred 6.11 Documentation.

Academic and Non-Profit Institutions

PolyPhred is available for free to researchers at academic and non-profit institutions. To aquire PolyPhred, please follow this procedure:

  1. Read the Academic License Agreement, and fill in and submit the request form.

  2. Within a few days, you will receive an email message with a user ID and password that will allow you to download PolyPhred.

  3. When you have the password, click on the appropriate download link below.

Commercial Businesses

Commercial businesses wanting to aquire PolyPhred are required to purchase a commercial license agreement.

  1. Please contact University of Washington TechTransfer Digital Ventures and follow the link "Express Licenses". Specific information about PolyPhred is here.

  2. When we receive confirmation from TechTransfer Digital Ventures, you will receive an email message with a user ID and password that will allow you to download PolyPhred.

  3. When you have the password, click on the appropriate download link below.

 

Download PolyPhred 6.11 Beta

To download PolyPhred, click on one of the links below and enter the user ID and password:
GNU/Linux x86 Download
GNU/Linux x86 64-bit Download
Mac OS X PowerPC Download
Mac OS X Intel x86 Download
Solaris SPARC Download
IBM AIX PowerPC Download
DEC Alpha Download

For security, the passwords to aquire PolyPhred change weekly. If the password you have has expired, please request a new one by emailing Jennifer Mercado (jmercado@u.washington.edu).

Instructions

The downloaded file is a UNIX tape archive compressed with gzip. It contains:

bin/
   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.
   phredPhrapa script written in Perl that runs the programs phred and phrap
doc/
   polyphred.html   the PolyPhred documentation in html format.

To unzip and untar the file, open a terminal window, change to the directory where you saved the archive and run the command: 

  gunzip -c polyphred-6.11-binary-*.tar.gz | tar xvf -

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 this files.

Download for all platforms

Move example.tar.gz to an empty directorty and use these commands to unpack the file: 

 gunzip example.tar.gz
 tar xf example.tar

These commands will generate a directory named example, which contains the sample data, and a text file called EXAMPLE.doc.

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

Download for all platforms

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

 gunzip csft2.tar.gz
 tar xf csft2.tar

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