GitHub - bmajoros/MUMMIE: MUltivariate Markov Modeling Inference Engine

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MUltivariate Markov Modeling Inference Engine

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Name		Name	Last commit message	Last commit date
Latest commit History 39 Commits
perl		perl
python @ 0f2090f		python @ 0f2090f
.gitmodules		.gitmodules
BackwardAlgorithm.C		BackwardAlgorithm.C
BackwardAlgorithm.H		BackwardAlgorithm.H
BaumWelch.C		BaumWelch.C
BaumWelch.H		BaumWelch.H
BaumWelchMT.C		BaumWelchMT.C
BaumWelchMT.H		BaumWelchMT.H
ComponentViterbi.C		ComponentViterbi.C
ComponentViterbi.H		ComponentViterbi.H
Emission.C		Emission.C
Emission.H		Emission.H
EmissionLoader.C		EmissionLoader.C
EmissionLoader.H		EmissionLoader.H
EmissionSequence.C		EmissionSequence.C
EmissionSequence.H		EmissionSequence.H
FastForward.C		FastForward.C
FastForward.H		FastForward.H
FastViterbi.C		FastViterbi.C
FastViterbi.H		FastViterbi.H
ForwardAlgorithm.C		ForwardAlgorithm.C
ForwardAlgorithm.H		ForwardAlgorithm.H
HMM.C		HMM.C
HMM.H		HMM.H
HMMGraph.C		HMMGraph.C
HMMGraph.H		HMMGraph.H
HMMbuilder.C		HMMbuilder.C
HMMbuilder.H		HMMbuilder.H
HMMreader.C		HMMreader.C
HMMreader.H		HMMreader.H
IntervalDecoder.C		IntervalDecoder.C
IntervalDecoder.H		IntervalDecoder.H
Kmeans.C		Kmeans.C
Kmeans.H		Kmeans.H
LICENSE		LICENSE
ParallelBaumWelch.C		ParallelBaumWelch.C
ParallelBaumWelch.H		ParallelBaumWelch.H
Posterior.C		Posterior.C
Posterior.H		Posterior.H
PosteriorViterbi.C		PosteriorViterbi.C
PosteriorViterbi.H		PosteriorViterbi.H
README		README
Schema.C		Schema.C
Schema.H		Schema.H
SequenceSet.C		SequenceSet.C
SequenceSet.H		SequenceSet.H
State.H		State.H
TieEvent.C		TieEvent.C
TieEvent.H		TieEvent.H
TieProfile.C		TieProfile.C
TieProfile.H		TieProfile.H
UnscaledBackwardAlgorithm.C		UnscaledBackwardAlgorithm.C
UnscaledBackwardAlgorithm.H		UnscaledBackwardAlgorithm.H
UnscaledBaumWelch.C		UnscaledBaumWelch.C
UnscaledBaumWelch.H		UnscaledBaumWelch.H
UnscaledForwardAlgorithm.C		UnscaledForwardAlgorithm.C
UnscaledForwardAlgorithm.H		UnscaledForwardAlgorithm.H
UnscaledHMM.C		UnscaledHMM.C
UnscaledHMM.H		UnscaledHMM.H
UnscaledHMMreader.C		UnscaledHMMreader.C
UnscaledHMMreader.H		UnscaledHMMreader.H
analyze-groups.pl		analyze-groups.pl
analyze-iulian-clusters.pl		analyze-iulian-clusters.pl
assemble-transcripts.pl		assemble-transcripts.pl
auto-motifs.pl		auto-motifs.pl
average-chains.pl		average-chains.pl
average-fastb.pl		average-fastb.pl
baum-welch.C		baum-welch.C
bg.hmm		bg.hmm
centroids-to-pca.pl		centroids-to-pca.pl
change-track-name.pl		change-track-name.pl
check-overlap.pl		check-overlap.pl
classify.C		classify.C
cluster-fastb.C		cluster-fastb.C
combine-miRNA-predictions.pl		combine-miRNA-predictions.pl
cons.schema		cons.schema
describe-centroids.pl		describe-centroids.pl
deterministic-trainer.C		deterministic-trainer.C
discretize.C		discretize.C
drop-continuous.C		drop-continuous.C
entropy.C		entropy.C
eval-permute.pl		eval-permute.pl
eval.pl		eval.pl
expand-miRNA-seeds.pl		expand-miRNA-seeds.pl
extract-chain.C		extract-chain.C
extract-gff-intervals.C		extract-gff-intervals.C
extract-motifs.C		extract-motifs.C
extract-state-sequences.C		extract-state-sequences.C
fasta-to-fastb.pl		fasta-to-fastb.pl
fastb-add-folding-noave.pl		fastb-add-folding-noave.pl
fastb-add-folding.pl		fastb-add-folding.pl
fastb-add-wig-track.C		fastb-add-wig-track.C
fastb-add-wig.pl		fastb-add-wig.pl
fastb-diff.py		fastb-diff.py
fastb-extract-tracks-dir.pl		fastb-extract-tracks-dir.pl
fastb-extract-tracks.pl		fastb-extract-tracks.pl
fastb-length.C		fastb-length.C
fastb-rename-track.pl		fastb-rename-track.pl
fastb-scale-track.pl		fastb-scale-track.pl

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MUMMIE version 1.1

To compile MUMMIE:

make all

Please set environment variable "MUMMIE" to point to this directory.

Please add "$MUMMIE/python" to your PYTHONPATH

Please add "$MUMMIE/perl" to your PERLLIB