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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 purpose.


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.

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