PILER-64

"PILER is public domain software for analyzing repetitive DNA found in genome sequences." - http://drive5.com/piler/

PILER was originally conceived and implemented by Robert Edgar and Eugene Myers. This derivative version of PILER adds support for 64-bit architectures, and should run to completion without malloc errors on genomes with large, diverse repeat landscapes. Only changes to memory allocation code have been made, so results should be consistent for input data that successfully runs with the version distributed at drive5.com. If you notice discrepencies, please raise an issue here on GitHub.

License

The modifications to PILER distributed here are released to the public domain.

Original License

The PILER software, including object and source code and documentation, is hereby donated to the public domain. Disclaimer of warranty THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.

Citing

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

Name		Name	Last commit message	Last commit date
Latest commit History 8 Commits
Makefile		Makefile
README.md		README.md
annot.cpp		annot.cpp
annotedge.cpp		annotedge.cpp
bitfuncs.h		bitfuncs.h
cons.cpp		cons.cpp
contigs.cpp		contigs.cpp
crisp.cpp		crisp.cpp
findcc.cpp		findcc.cpp
gff.cpp		gff.cpp
gff2.cpp		gff2.cpp
gffset.cpp		gffset.cpp
gffset.h		gffset.h
glix.cpp		glix.cpp
glix.h		glix.h
hash.cpp		hash.cpp
iix.cpp		iix.cpp
iix.h		iix.h
log.cpp		log.cpp
main.cpp		main.cpp
makeannot.cpp		makeannot.cpp
mem.cpp		mem.cpp
options.cpp		options.cpp
params.h		params.h
piler2.h		piler2.h
progress.cpp		progress.cpp
quit.cpp		quit.cpp
readafa.cpp		readafa.cpp
readhits.cpp		readhits.cpp
readmfa.cpp		readmfa.cpp
readmotif.cpp		readmotif.cpp
readreps.cpp		readreps.cpp
readtrs.cpp		readtrs.cpp
tan.cpp		tan.cpp
tanmotif2fasta.cpp		tanmotif2fasta.cpp
tr.cpp		tr.cpp
trs.cpp		trs.cpp
trs2fasta.cpp		trs2fasta.cpp
types.h		types.h
usage.cpp		usage.cpp
utils.cpp		utils.cpp
utils_linux.cpp		utils_linux.cpp
utils_unix.cpp		utils_unix.cpp
utils_win32.cpp		utils_win32.cpp
writecrisp.cpp		writecrisp.cpp
writefasta.cpp		writefasta.cpp
writeimages.cpp		writeimages.cpp
writepiles.cpp		writepiles.cpp
writetrs.cpp		writetrs.cpp

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PILER-64

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