bin/ipestimate
conf/gHMM.xml
conf/gHMM_nscan.xml
conf/gtf_map_utr_hacked_inter.xml
conf/gHMM_est.xml
conf/gtf_map_hacked_inter.xml
conf/gHMM_utr.xml
conf/gtf_map.xml
conf/gHMM_inter.xml
conf/gtf_map_utr.xml
conf/gHMM_nscan_est.xml
conf/iPE_instance.xml
doc/wiki/ipe_dataflow.jpg
doc/fitting_geom.pdf
doc/fitting_geom.tex
doc/example/gHMM.xml
doc/example/instance.xml
doc/example/gtf_map.xml
doc/example/chr20.eval.short.gtf
doc/example/chr20.estseq.short.fa.bz2
doc/example/chr20.masked.short.fa.bz2
doc/example/chr20.conseq.short.fa.bz2
doc/example/chr20.arrayseq.short.fa.bz2
doc/example/chr20.short.align.bz2
doc/book/Makefile
doc/book/background/models.tex
doc/book/background/hacks.tex
doc/book/background/gsp.tex
doc/book/background/main.tex
doc/book/background/hmms.tex
doc/book/background/parsing.tex
doc/book/iPE-User-Guide.pdf
doc/book/preliminaries/xml.tex
doc/book/preliminaries/terms.tex
doc/book/preliminaries/parameters.tex
doc/book/preliminaries/main.tex
doc/book/preliminaries/begin.tex
doc/book/preliminaries/dtd.tex
doc/book/preliminaries/gtf.tex
doc/book/preface/main.tex
doc/book/timehmm.graffle
doc/book/main.bib
doc/book/genscanhmm.ps
doc/book/histogram.eps
doc/book/instance.eps
doc/book/fomc.graffle
doc/book/annprocess.eps
doc/book/timehmm.eps
doc/book/mc.graffle
doc/book/acknowledgements.tex
doc/book/histogram.pdf
doc/book/ghmm.eps
doc/book/introduction/whatispe.tex
doc/book/introduction/main.tex
doc/book/introduction/whatisipe.tex
doc/book/introduction/whatcanitdo.tex
doc/book/genscanhmm.eps
doc/book/histogram.ps
doc/book/deeper/exploring.tex
doc/book/deeper/main.tex
doc/book/deeper/durations.tex
doc/book/deeper/process.tex
doc/book/deeper/sequence.tex
doc/book/mdd.pdf
doc/book/ghmmfiles/main.tex
doc/book/hmm.eps
doc/book/main.tex
doc/book/mdd.ps
doc/book/genscanhmm.pdf
doc/book/gettingstarted/outputfiles.tex
doc/book/gettingstarted/dirs.tex
doc/book/gettingstarted/running.tex
doc/book/gettingstarted/main.tex
doc/book/gettingstarted/inputfiles.tex
doc/book/installation/manual.tex
doc/book/installation/rpm.tex
doc/book/installation/main.tex
doc/book/appendix/featuremapref.tex
doc/book/appendix/ghmmref.tex
doc/book/annprocess.graffle
doc/book/sidebar.sty
doc/book/mdd.eps
doc/book/xmldescr.oo3
doc/book/iPE.sty
doc/book/mc.eps
lib/iPE/Smoother.pm
lib/iPE/Instance.pm
lib/iPE/XML/Object.pm
lib/iPE/XML/DocObject.pm
lib/iPE/XML/Wrappers.pm
lib/iPE/FeatureMapping.pm
lib/iPE/Sequence.pm
lib/iPE/Annotation.pm
lib/iPE/SequenceReader/NoLoad/Align.pm
lib/iPE/SequenceReader/NoLoad/Raw.pm
lib/iPE/SequenceReader/NoLoad/FASTA.pm
lib/iPE/SequenceReader/Load/Raw.pm
lib/iPE/SequenceReader/Load/FASTA.pm
lib/iPE/SequenceReader/Load.pm
lib/iPE/SequenceReader/NoLoad.pm
lib/iPE/Annotation/Transcript.pm
lib/iPE/Annotation/NullRegion.pm
lib/iPE/Annotation/Feature.pm
lib/iPE/Annotation/NullDefinition.pm
lib/iPE/Annotation/SegmentedAnnotation.pm
lib/iPE/Annotation/Segment.pm
lib/iPE/Util/BoundaryCoordinate.pm
lib/iPE/Util/Overlap/Node.pm
lib/iPE/Util/DNATools.pm
lib/iPE/Util/Overlap.pm
lib/iPE/Util/Output.pm
lib/iPE/Util/Interval.pm
lib/iPE/State.pm
lib/iPE/Comments.pm
lib/iPE/gHMM.pm
lib/iPE/Smoother/Pseudocount.pm
lib/iPE/Smoother/Null.pm
lib/iPE/Smoother/Kernel.pm
lib/iPE/Smoother/Gaussian.pm
lib/iPE/AnnotationPlugin.pm
lib/iPE/FeatureMap.pm
lib/iPE/SequenceReader.pm
lib/iPE/Options.pm
lib/iPE/AnnotationPlugin/GTFPlugin.pm
lib/iPE/Sequence/Cola.pm
lib/iPE/Sequence/Repeat.pm
lib/iPE/Sequence/Est.pm
lib/iPE/Sequence/Malign.pm
lib/iPE/Sequence/Region.pm
lib/iPE/Sequence/Cons.pm
lib/iPE/Sequence/Tile.pm
lib/iPE/Sequence/Asest.pm
lib/iPE/Sequence/Dna.pm
lib/iPE/Globals.pm
lib/iPE/Levels.pm
lib/iPE/Model.pm
lib/iPE/Model/Emission.pm
lib/iPE/Model/DurationDistribution/DEFINED.pm
lib/iPE/Model/DurationDistribution/CONSTANT.pm
lib/iPE/Model/DurationDistribution/GEOMETRIC.pm
lib/iPE/Model/Duration.pm
lib/iPE/Model/Emission/JUMPLUT.pm
lib/iPE/Model/Emission/MARG_WAM.pm
lib/iPE/Model/Emission/LUT.pm
lib/iPE/Model/Emission/ELUT.pm
lib/iPE/Model/Emission/WAM.pm
lib/iPE/Model/Emission/WMM.pm
lib/iPE/Model/Emission/ASM.pm
lib/iPE/Model/Emission/SPLIT.pm
lib/iPE/Model/Emission/SDT.pm
lib/iPE/Model/Emission/WWAM.pm
lib/iPE/Model/Emission/CDS.pm
lib/iPE/Model/Emission/ISO.pm
lib/iPE/Model/Emission/SIG.pm
lib/iPE/Model/ISO.pm
lib/iPE/Model/EmissionChain.pm
lib/iPE/Model/DurationDistribution.pm
lib/iPE/Model/DurationSubmodel.pm
lib/iPE/Estimator.pm
lib/iPE/State/Transitions.pm
lib/iPE/State/PseudoTransition.pm
lib/iPE/State/AltSplice/MultiThreePrime.pm
lib/iPE/State/AltSplice/OptExon.pm
lib/iPE/State/AltSplice/MultiSite.pm
lib/iPE/State/AltSplice/MultiFivePrime.pm
lib/iPE/State/AltSplice.pm
lib/iPE/State/PseudoState.pm
lib/iPE.pm
scripts/finalize_nscan_parameters.pl
scripts/convert_old_gHMM_to_new_format.pl
scripts/generate_cv_sets.pl
scripts/generate_model_cv_sets.pl
scripts/make_blastzdb_from_reads.pl
scripts/make_instance_file.pl
scripts/validate_gHMM.pl
sgml/parameter_file.dtd
sgml/iPE_instance.dtd
sgml/feature_map.dtd
sgml/gHMM.dtd
install_ipe.sh
iPE.xs
Makefile.PL
MANIFEST
README
RPM/ipe.spec
TODO
