PolyPhred Information

If you have technical questions or problems with PolyPhred, please contact Ian Robertson at polyphred@u.washington.edu. For questions about licensing and registration, please contact Jennifer Mercado at jmercado@u.washington.edu.

The programs Phred and Phrap are absolutely required for running PolyPhred, and Consed is highly recommended. These programs are developed by another group at the University of Washington.

Please visit the Phred/Phrap/Consed site for information on obtaining these programs.

If you have questions about these programs:
PhredBrent Ewingbge@u.washington.edu
PhrapPhil Greenphg@u.washington.edu
ConsedDavid Gordongordon@genome.washington.edu

Release history for PolyPhred version 6

PolyPhred 6.11 beta - released May 14, 2007

PolyPhred 6.10 beta - released April 11, 2007

PolyPhred 6.02 beta

PolyPhred 6.0 beta

Release history for PolyPhred version 5

PolyPhred Version 5.04 - released February 7, 2006.
Added an option to the -ms flag (-ms x) which allows the user to demote the score of putative SNPs that are found within microsatellite repeat regions.
Improved the microsatellite detection algorithm so that imperfect repeats can be detected.
Added a new program, polygen, to the package. The tool can be used to generate 'phd' and 'poly' files without the use of Phred. The base calls come from the ABI base-calling software and are extraced directly from the chomat files.

PolyPhred Version 5.03 - released September 29, 2005.
Corrected a error in the code that could in some situations affect the scoring of sites.
Also fixed a problem with the function that searches for the most recent ace file when the -ace flag is not used. In previous versions, if the -ace flag was not used, an ace file that did not have a number on the end of the file name were ignored.

PolyPhred Version 5.02 - released July 11, 2005.
In this version, flaws in the -refcomp and -snp functions were corrected, and the ability to handle file names with dashes was reimplemented.
A problem in sudophred was also corrected.

PolyPhred Version 5.01 - released June 10, 2005.
This version incorporated a new algorithm for scoring putative SNP sites. The new algorithm results in a significant reduction in the number of false positives.

Release history for PolyPhred Version 4.2

PolyPhred Version 4.29 - released February 28, 2005.
In this version, a problem with the -group flag was fixed.

PolyPhred Version 4.28 - released February 9, 2005.
In this version, a fix was made to correct for a rare anomaly in the poly files, the appearance of a zero in the first line.

PolyPhred Version 4.27 - released November 29, 2004.
In this version, add flexibility to the -s flag, so that the source ID can be either specified either by a delimiter or by location. Also, directory and file names can now contain dashes (-).
The sudophred utility now writes the chromat file in scf format rather than the ABI format.

PolyPhred Version 4.26 - released August 3, 2004.
In this version, improvements to the -s function were made, and problems with with the -ref and -refcomp functions were corrected.

PolyPhred Version 4.25 - released June 16, 2004.
In this version, problems with the -s function and with the -refcomp function were corrected.

PolyPhred Version 4.24 - released May 11, 2004.
In this version, problems with the -s function and with the -o flag were corrected. Also in this version was added the ability to designate a data directory structure other than the one used by Consed.

PolyPhred Version 4.23 - released March 2, 2004.
This version fixed a problem in the COMMAND_LINE section of the output file when the -refcomp flag is used.

PolyPhred Version 4.22 - released February 11, 2004.
This version fixes a problem with the positions of manual genotype tags in the output file.

PolyPhred Version 4.21 - released February 5, 2004.
This version fixes some problems with the -ref and -refcomp functions.

PolyPhred Version 4.20 - released January 21, 2004.
New features in this version include:

  1. PolyPhred now uses a 100-point scoring system to rank the polymorphic sites. The old six-point ranking system is still available for backward compatibility.

  2. Multiple sequences of the same DNA sample can be combined to provide more accurate genotyping, using the -source flag.

  3. The user to specify a reference sequence rather than the consensus sequence as the sequence standard, using the -refcomp flag.

  4. PolyPhred searches for homozygous insertion/deletion (indel) sites as well as heterozygous indels.

  5. Indel sites can be tagged manually for accurate positioning and genotyping.

  6. An option to mark simple microsatellite sequences to help identify potential problem areas is available.

  7. An option to write the output file in XML format is provided.

PolyPhred Version 4.00 - released January 7, 2002.
New features in this version include:

  1. There are several new command-line flags for controlling the operation of PolyPhred. All flags, including the -ace flag, are now optional.

  2. New blocks have been added to the output report to provide more information.

  3. Three types of manually-applied tags can be captured from ACE and PHD files and reported in the output.

  4. If a reference sequence is used in the assembly process with Phred and Phrap, PolyPhred can report the positions of polymorphic sites relative to the reference sequence.

  5. PolyPhred can be customized to suit user preferences by creating a .polyphredrc file. This file can be used to set defaults to preferred values, and to identify manual tags for manual tag tracking.

  6. PolyPhred can generate a navigation file that facilitates visualization of polymorphic sites within the Consed application.

  7. PolyPhred can search sample sequences for evidence of insertion/deletion (indel) polymorphisms.

  8. PolyPhred now runs about three times faster than previous versions, and uses about one-third the memory.

  9. PolyPhed is now available for HP systems.

Release history for PolyPhred Version 4.0

Version 4.07 - June 2, 2003
This version coordinates SNP and indel tags with the latest version of Consed (version 13). Also, positions marked with a 'column genotype' tag are now listed in the POLY section of the output file.

Version 4.06 - February 24, 2003
Corrected a bug that was sometimes evident when a user placed a 'column genotype' tag on the consensus position. This tag can be used to force PolyPhred to genotype a column of sites and report the genotypes in the COLUMN_GENOTYPE section of the output file. If a putative heterozygote was detected by PolyPhred in such a column, version 4.05 reports the site as heterozygous in the GENOTYPE section, but homozygous in the COLUMN_GENOTYPE section.
In addition, an error in the time stamp reported in the ouput file was corrected.

Version 4.05 - January 28, 2002
In this version, a bug the was introduced in version 4.04 was corrected.

Version 4.04 - January 25, 2002
This version fixes a bug in writing the navigation file that was inadvertantly introduced in version 4.03. This version also modified to allow the user to specify a path for the navigation file and output file so that these files can be written to any valid directory.

Version 4.03 - January 22, 2002
This version fixes a bug that caused PolyPhred in rare situations to incorrectly genotype heterozygous sites.

Version 4.02 - January 18, 2002
This version fixes a bug that caused PolyPhred to fail to mark some columns in which only homozygous mismatches are present.

Version 4.01 - January 11, 2002
This version fixes a bug that caused PolyPhred to fail if sample sequences in the ACE file contained characters other than A, C, G, T, N or * (or their lower case). The problem can occur you are using cloned sequences with the Phrap vector filtering option on. With this option on, Phrap replaces the vector sequence with x's.


A program called sudophred is include with Polyphred version 4.05. This program generates phd and poly files from sequences in FASTA format.

On March 26, 2002, a bug was found in sudophred and fixed. The problem was with the -r option. If you are trying to use sudophred, and the -r option is not working, email Jennifer Mercado for a new access password.

Version 2.0 was release on March 25, 2003. This version generates mock trace files in addition to the phd and poly files.
The new version also corrects a bug that existed in the previous version. The bug appeared when a user wanted multiple phd and poly files from a FASTA file containing more than one sequence. With the previous version, the phd information for these sequences would be concatenated into a single file. The poly information is also written into a single file.

Version 3.0 was release on November 29, 2004. This version writes the mock trace file in scf format rather than the ABI format.

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