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	Control/Monad	Our very own *lazy* randomness monad	Jun 19, 2012
	SearchStrategies	create and use a version of 'shuffle' that's in the Rand monad	Jun 29, 2012
	data	adding beta dat files	Jan 9, 2012
	otherdocs	more on local alignments	Jul 9, 2012
	scripts	beta probs incorporated, ruby script to generate them as well.	Jan 5, 2012
	testing	Fix a div-by-zero error	Jul 5, 2012
	.gitignore	ignore mrfy-bench directory	May 2, 2013
	BENCH	instructions for aging tenured faculty	May 6, 2013
	Beta.hs	sandwich.hmm+ works	Jul 10, 2012
	BetaProps.hs	First cut at QuickChecking the [StrandPair] -> [BetaStrand] conversion.	Jul 7, 2012
	CommandArgs.hs	Control the number of times viterbi runs. (For the Oracle.)	May 26, 2013
	Constants.hs	Update to work with GHC 7.8.	Jun 1, 2014
	ConstantsGen.hs	Modest performance improvements by using Unboxed vectors.	Jun 3, 2012
	DEPENDENCIES	'bio' not 'bio-haskell'	Feb 23, 2012
	DevNotes.txt	Kill alpha argument to viterbi.	May 11, 2012
	Fasta.hs	ghc --make thinks an empty .hs file has a 'main' function. doy.	Oct 7, 2011
	FileOps.hs	Control the number of times viterbi runs. (For the Oracle.)	May 26, 2013
	HMMArby.hs	Prohibit empty HMMs. Fixed a bug in Viterbi thanks to QuickCheck	Jul 3, 2012
	HMMPlus.hs	Update to work with GHC 7.8.	Jun 1, 2014
	HMMProps.hs	Prohibit empty HMMs. Fixed a bug in Viterbi thanks to QuickCheck	Jul 3, 2012
	HyperTriangles.hs	added '-test all-props' option, which is a lie	Jun 23, 2012
	LazySearchModel.hs	made a benchmark more reasonable. added some comments to LazySearchModel	Jun 30, 2012
	MRFTypes.hs	sandwich.hmm+ works	Jul 10, 2012
	Main.hs	refactored main code and mkfile	May 10, 2012
	NonUniform.hs	genetic algorithms still suck.	Feb 16, 2012
	ParRandom.hs	Our very own *lazy* randomness monad	Jun 19, 2012
	ParsecHelper.hs	Removed PADS dependency (woohoo!)	May 26, 2012
	Perturb.hs	export approxEq	Jul 5, 2012
	PrefixMemo.hs	added file PrefixMemo which is a step toward memoization based on lis…	Mar 30, 2013
	PsiPred.hs	Removed PADS dependency (woohoo!)	May 26, 2012
	README	DEPENDENCIES keeps track of what smurf2 needs to compile. Main.hs has…	Oct 7, 2011
	RunPsiPred.hs	Removed PADS dependency (woohoo!)	May 26, 2012
	Score.hs	Update to work with GHC 7.8.	Jun 1, 2014
	SearchStrategy.hs	Fix a div-by-zero error	Jul 5, 2012
	Setup.hs	First pass at a cabal file. Does NOT yet work.	Mar 12, 2012
	ShowAlignment.hs	type HMMState is now StateLabel	Jun 27, 2012
	Shuffle.hs	turn on warnings for Shuffle.hs	Jun 29, 2012
	StochasticSearch.hs	Control the number of times viterbi runs. (For the Oracle.)	May 26, 2013
	TODO	more refactoring from NR	Mar 11, 2012
	V2.hs	higher-order Viterbi *without* intermediate allocation (and inlined)	Jul 10, 2012
	Viterbi.hs	added ViterbiPlusX to the Oracle	May 26, 2013
	Wrappers.hs	Modest performance improvements by using Unboxed vectors.	Jun 3, 2012
	ghc-opts	fixed bug in mkfile/ghc-opts; removed many trace calls	Jun 3, 2012
	mkfile	AG is lazy.	May 17, 2013
	mrfy.cabal	optimize	Apr 29, 2013
	notes.txt	use my Viterbi, first pass at StochasticSearch, include some notes	Nov 16, 2011
	session.vim	vim-fu	Apr 29, 2013
	sources.txt	added sources.txt for cabal-meta	Jun 19, 2012
	test.hmm+	initial import for github	Sep 8, 2011
	test.ss2	initial import for github	Sep 8, 2011