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       glam2-purge - Removes redundant sequences from a FASTA file


       glam2-purge file score [options]


       glam2-purge is a modified version of Andrew Neuwald´s purge program
       that removes redundant sequences from a FASTA file. This is recommended
       in order to prevent highly similar sequences distorting the search for
       motifs. Purge works with either DNA or protein sequences and creates an
       output file such that no two sequences have a (gapless) local alignment
       score greater than a threshold specified by the user. The output file
       is named <file>.<score>. The alignment score is based on the BLOSUM62
       matrix for proteins, and on a +5/-1 scoring scheme for DNA. Purge can
       also be used to mask tandem repeats. It uses the XNU program for this


           Sequences are DNA (default: protein).

           Use blast heuristic method (default for protein).

           Use an exhaustive method (default for DNA).

           Keep first sequence in the set.

           Use xnu to mask protein tandem repeats.


       glam2(1), glam2format(1), glam2mask(1), glam2scan(1), xnu(1)

       The full Hypertext documentation of GLAM2 is available online at or on this computer in


       Purge was written by Andy Neuwald and is described in more detail in
       Neuwald et al., "Gibbs motif sampling: detection of bacterial outer
       membrane protein repeats", Protein Science, 4:1618–1632, 1995. Please
       cite it if you use Purge.

       If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL
       Bailey (2008) Discovering sequence motifs with arbitrary insertions and
       deletions, PLoS Computational Biology (in press).


       Andrew Neuwald
           Author of purge, renamed glam2-purge in Debian.

       Martin Frith
           Modified purge to be ANSI standard C and improved the user

       Timothy Bailey
           Modified purge to be ANSI standard C and improved the user

       Charles Plessy <>
           Formatted this manpage in DocBook XML for the Debian distribution.


       The source code and the documentation of Purge and GLAM2 are released
       in the public domain.