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PILER-CR: detection of CRISPR repeats in bacterial genomes
See here for PILER-CR.
 
About PILER
 
PILER is public domain software for analyzing repetitive DNA found in genome sequences.

Downloads
Click here to download PILER source code only, 34 kb file, tarball (.tar.gz) format. 

Click here to download Mac OSX source and binaries for PALS and PILER.

Click here to download the rm2gff.py and trs_report.py python scripts.

You will also need MUSCLE and a whole-genome local aligner. You can use PALS for this, but please note that PALS is considered obsolete and is no longer supported. See the PALS home page for discussion.

Documentation
 Manual as a PDF file
Manual as a web page

Citing PILER
Please cite this paper:

R.C. Edgar and E.W. Myers, PILER: identification and classification of genomic repeats.
Bioinformatics. 2005 Jun 1;21 Suppl 1:i152-i158