7fec8d936d6c4de439ae8d1ffacea7f6 *DESCRIPTION
e385f9bf3a955b64b71ba4c67faca4e8 *NAMESPACE
5b88e2c55a47dcc95b57bfed91543530 *R/FitGMLD.R
624c167355e30b960e015be5db2d351a *R/GeneDrops.R
1a0618eb35d2c31b8c7dfcbd1ab2e2ef *R/read.pedfile.R
95c4858db59e9b6151a3fe8a104961e2 *R/write.parfile.R
862d8a7652d589f3b5324a163702b53b *R/write.pedfile.R
ed97d6001f8ebeb51dbadf0e6215f6f6 *R/zzz.R
47e923ef8c3be722612f7263496ea4a1 *data/exdat.rda
1c464f45880aca4627241822acc12d40 *inst/NEWS
22299e285e78cd73fe4aba72f621d93b *inst/java/GeneDrops.java
bcaa1efd9c1995208d210d478c7944bc *inst/java/JPSGCS.jar
3b385b0007dd3a1fb6b09428dde49cbd *inst/java/jpsgcs/alun/linkage/LinkageIndividual.java
7ff58f24b4b4322b1987e381ac092b2c *inst/java/jpsgcs/alun/linkage/LinkagePedigreeData.class
55fb58849a3f90dd83d50acae057c212 *inst/java/jpsgcs/alun/linkage/LinkagePedigreeData.java
8b00b43b0c6cf152c6c6aeb155e5b4c3 *java/ApproxGCHap.java
d32239bcb673463ab874e80d47fae504 *java/COPYING
457246dc88ff1845930884469a8cb9e8 *java/CheckErrors.java
61bf4af4d06c2ba768b997d75f4f8475 *java/CheckFormat.java
f0c538b45549b202d791b3def993ccbb *java/CheckParameters.java
dfb87ecad11319a51109f40a24530749 *java/CheckPedigree.java
2a51ff1b4079bcc402aa330c50d6b57c *java/CheckTriplets.java
b4e6781dadb8adb39f728b733073106a *java/CliquesToAdj.java
a3a6ecba5782a7e6edd144687a3493a0 *java/CompileLDModel.java
b498dc39de8f862d60762c498215a965 *java/Complete.java
453f8d6cd37e4c43ebf9fec41e0eaf0e *java/DownCodeAlleles.java
ea92c1de417315985b0572aa9fc30036 *java/FitGM.java
ba11cadc402b74510e886361d47963ea *java/FitGMLD.java
3db5194a9b45fce4dd9ac125dfddf904 *java/FitGMLDNoWind.java
fff5760bc78160c706e18d26527baa06 *java/GCHap.java
3c44f55e4dcc98ae28ddfe5a0581d5bb *java/GeneCountAlleles.java
301039da7617b86b7d7f3adee10fb50b *java/GeneDrop.java
22299e285e78cd73fe4aba72f621d93b *java/GeneDrops.java
f53a947f904abe6747ed2e35accbb789 *java/GetPolymorphisms.java
fa5c65e6c90694fee8b6856665d74570 *java/HGS.java
01e9c94e71e9fe5653073c15e2922740 *java/HapMapToLinkage.java
efc080a9f78fadd17904c724e0096c65 *java/HetCutOff.java
0c5a53e37d7921f1ec78a57dbb66e83d *java/HetLods.java
421a547059bd3b8db3e1ad503a9c8206 *java/Heterozygosities.java
42389fffb6001da726683024738eb883 *java/HomozygousSGS.java
bcaa1efd9c1995208d210d478c7944bc *java/JPSGCS.jar
765a3e095dc469e804d6125f0281e078 *java/LDModelToGraph.java
db44866f6fc48ed0db93e165430fb523 *java/LinkageToFastPhase.java
ed71c01644cc895c5de886c75c814c50 *java/LinkageToPhase.java
4e4e00d1d059b98898f654dc160e2a98 *java/LocusLogLikelihoods.java
0c8d28819fc64860dc88a62e2f2c3d35 *java/MakePed.java
58b7e2f449ce26f01c765d575372dc9f *java/MakeProbands.java
42d982232e2e2f8536e17be4aea406dc *java/MaxTwoPointLods.java
219b0bfc5f8b424c174a5241940dad47 *java/McCheck.java
4519a76ab21d466491142892a232b632 *java/McKinship.java
25d66a5226eece2214edd6546fa08cff *java/McLinkage.java
8fb0ddafa7ef7260d1c6424dc0d0b45b *java/McMultiPoints.java
989de183e75598f14cd426ba8aa28e6b *java/McTLods.java
2214522989fec09acb35e95d76a9a69f *java/ObligateErrors.java
ff89dc2c2db5b0a6ce55a8cd1cfcdb72 *java/SGS.java
a4e8e08bfab452c365e76bdc39b9f599 *java/SelectKindreds.java
e353dd73d95cc54477e47755439833de *java/SelectLoci.java
25a455d73fd63e9d16d0a24065e752cf *java/SelectPedigrees.java
a3366679fed20953041a581d5c0b9df0 *java/SimHGS.java
b125e6337456e56ec91de5092edd495c *java/SimHomozygousSGS.java
d2a1273851e9e7d0057c8759d31fdb5a *java/SimSGS.java
6654fc6ff3014bcc3a7e7ae315b47d33 *java/TestRandom.java
5b3f5e5ede19c8bf9b0fd2b6d9eb86c9 *java/TransposeLinkage.java
07cc496078ea83fc01bebfcca7a1125e *java/Triangulate.java
d65a2f59ff474d1b9fcaf88112d15998 *java/TrimPed.java
df5b2c75a83bbf464a9f66e6c1bb5ee2 *java/TwoPointLods.java
3ca1e2c6f7d7972d91857fc7696f2c38 *java/ViewDAG.java
445701b2344b35beed4f1568a9e1446e *java/ViewGraph.java
693e4574e4a025f131fd929c4d4cb652 *java/ViewLinkPed.java
e80aa54c2cb1c52b8bb714c770ff282c *java/ViewPed.java
8780a4abb5d66d11c3f8bc7205da9e9e *java/ZeroLoopPed.java
ca3768f3e6c70fa4eb3272ac02913fa6 *java/cMorgansToTheta.java
28a51c362c7c1167bead673f2c28ff8a *java/jpsgcs/alun/animate/ActiveCanvas.java
019f399151314fc6443a02332072e405 *java/jpsgcs/alun/animate/BufferedCanvas.java
094a45fa33a34053954fdd8e615156b2 *java/jpsgcs/alun/animate/FrameQuitter.java
e9a7aa3aaa878fd4bd646815f623b685 *java/jpsgcs/alun/animate/Loop.java
0db8b72afec37d60761448eb686824f7 *java/jpsgcs/alun/animate/MouseKeyListener.java
3705016c0037c531bcfb62435b53399a *java/jpsgcs/alun/animate/Paintable.java
b6ee852533c83f576fd86d5218d3a3af *java/jpsgcs/alun/animate/ScrollWidget.java
5d62ccbe04b37afa41bfe6024d57c138 *java/jpsgcs/alun/animate/TransformListener.java
a4ec16e7ea5e65b2aac3e4eb285ffcfe *java/jpsgcs/alun/gchap/GeneticTrait.java
fb4d3ae3c3e0214132fd5ac4ceffb690 *java/jpsgcs/alun/gchap/Genotype.java
6b687913855d39a09dd597abf953999d *java/jpsgcs/alun/gchap/HapFormatter.java
ab6d5a46e051347254ff986f5d00c7f2 *java/jpsgcs/alun/gchap/HashOfHash.java
17688174592249b72205b37dee685601 *java/jpsgcs/alun/gchap/Locus.java
54fb4cd32ecc40adb4f56f72d0ef2c29 *java/jpsgcs/alun/gchap/Marker.java
41385410ae4e8d52ab1cfea99b8d1c15 *java/jpsgcs/alun/gchap/MarkerObservation.java
97f5e0fdbdde4561157edf2e1c26b234 *java/jpsgcs/alun/gchap/MarkerPhenotype.java
c840c1525c58b3975c9adf4480203eb9 *java/jpsgcs/alun/gchap/MultiLocus.java
b2088cab47ac3b7673458877f2037e4b *java/jpsgcs/alun/gchap/MultiLocusObservation.java
be6815f9505857e7b9fc72137171870f *java/jpsgcs/alun/gchap/MultiLocusPhenotype.java
925ace6d16d10df426cab77ba0f8652b *java/jpsgcs/alun/gchap/MultiLocusTrait.java
8bfe81cf7c0541253160057d4e75f6cd *java/jpsgcs/alun/gchap/Observation.java
5b11224d3759b8a5d161041a327fd610 *java/jpsgcs/alun/gchap/Phenotype.java
f7726f7b76172faa4368294b7f146169 *java/jpsgcs/alun/gchap/SNP.java
208c63a0d5b2c8f62bbe902349d47139 *java/jpsgcs/alun/gchap/Sorter.java
e84158967441240be73733ca63dbc10d *java/jpsgcs/alun/genio/BasicGeneticData.java
3b001ce4e454301acb9538ca872896d5 *java/jpsgcs/alun/genio/Family.java
4dee954b0346cf01acebaa911c4bd5db *java/jpsgcs/alun/genio/GeneticDataSource.java
20a336d5288ac9f31f3066285166f390 *java/jpsgcs/alun/genio/ParameterData.java
4b40b7fae9363bbfdfe3f01996590836 *java/jpsgcs/alun/genio/Pedigree.java
ab5ac0132252af1c8fdbd5566450271b *java/jpsgcs/alun/genio/PedigreeData.java
cf86c34d60cea785b812eaabe5510396 *java/jpsgcs/alun/graph/DAGLocator.java
d2fa8ef704dd1866034550699abea8d4 *java/jpsgcs/alun/graph/Derivatives.java
e7e7b4ee2e93d6a70d6143ff835f68a4 *java/jpsgcs/alun/graph/Graph.java
7b2f9a45598fe95cc397e65b646ecdbb *java/jpsgcs/alun/graph/GraphLocator.java
569e26c28b9a1301a7dde3ebdb2884dc *java/jpsgcs/alun/graph/GraphSkeleton.java
cd4d4d8239c2af44e938aa7d05460cc7 *java/jpsgcs/alun/graph/Graphs.java
3c66a8e402e8f12b6f769d9696cfdfc6 *java/jpsgcs/alun/graph/IdentityNetwork.java
c824b85e0ef006c325142d39ec2531b2 *java/jpsgcs/alun/graph/LocalLocator.java
ecb40ae71c089b34b8d30abe904efe9a *java/jpsgcs/alun/graph/LocatedGraph.java
e85ef4aa0308267e3ecdcd793651778c *java/jpsgcs/alun/graph/LocatedMaskedGraph.java
53169cbcaad3a0b1d110c77fc5c04022 *java/jpsgcs/alun/graph/MaskedGraph.java
503abd1baab67a5e02b869126e95cc62 *java/jpsgcs/alun/graph/MutableGraph.java
87d5644c3a3c814b02886e9e061388f9 *java/jpsgcs/alun/graph/Network.java
a67075cbc65f50a566e21da588b2839a *java/jpsgcs/alun/graph/NetworkMask.java
e949283d9673b5d3455875f3f36fde1d *java/jpsgcs/alun/graph/Parameter.java
e8447cc67c211e170ff5d60eeda002ec *java/jpsgcs/alun/graph/Point.java
69e61877c7dde6305cc00fbd09523d81 *java/jpsgcs/alun/graph/RootedLocalLocator.java
567fea9ff16e3961a6ed33792bb4f851 *java/jpsgcs/alun/hashing/IdentityHashMap.java
b6cd6e207e2c3540460d75384661d06e *java/jpsgcs/alun/hashing/RandomIdentitySet.java
670710728c0e9a9bfa3c843d03522869 *java/jpsgcs/alun/jtree/AbstractJTreeSampler.java
dea5953140ae57b6ef6d989f55c063e7 *java/jpsgcs/alun/jtree/CardinalitySorter.java
248f351641c06f303fad5775f6fb1094 *java/jpsgcs/alun/jtree/Clique.java
a3f6ca5b5cb95d66f9e439d56ab79654 *java/jpsgcs/alun/jtree/CliqueScorer.java
fd1c0d7f2c444af977a4abd4612d7a23 *java/jpsgcs/alun/jtree/DataMatrix.java
17f789cb2cb937ec0d2479f3d813745b *java/jpsgcs/alun/jtree/DiscreteData.java
0a1966d2886ddf5c29813a33b4fd164e *java/jpsgcs/alun/jtree/GraphNotDecomposableException.java
1f3b1615554083f9d2b712601c579fd3 *java/jpsgcs/alun/jtree/IntegerMatrix.java
5ab75425096f3d7f47a601e2a9f58bad *java/jpsgcs/alun/jtree/JTree.java
15c24379f84bf40a25c6c41e7c15fdde *java/jpsgcs/alun/jtree/JTreeSampler.java
1b852176c99599cddc8bc7b021a671d3 *java/jpsgcs/alun/jtree/JTrees.java
a8e8a9c94f4a8c861b19831bb4669cf8 *java/jpsgcs/alun/jtree/MultinomialMLEScorer.java
61c88654e010c9ee72648fbcf9ae424f *java/jpsgcs/alun/jtree/OnePairSampler.java
90e035e0e6b9bc862e349343fa297f22 *java/jpsgcs/alun/jtree/OrderedJTree.java
9f793635a811f617f0a5ceabf9ebb62b *java/jpsgcs/alun/jtree/ProperIntervalJTree.java
4657b22aa94775d4bb1f79429cd60d2c *java/jpsgcs/alun/jtree/PruferSorter.java
84bb5b597946e0e569dfbc9c69e9ef13 *java/jpsgcs/alun/jtree/Separator.java
e1b5c492ea1c5128048cc9596fe9459b *java/jpsgcs/alun/jtree/UniformDecomposable.java
2a11fe0fd8fb094f12f44b93730f2c73 *java/jpsgcs/alun/jtree/UniformJTree.java
87aae3f733f9b2374c874acfcfae16c8 *java/jpsgcs/alun/linkage/AffectionStatusLocus.java
0c71eca2abf39b389f906a2dcea279be *java/jpsgcs/alun/linkage/AffectionStatusPhenotype.java
ddff13d8ddfb9a4d12313119b40aa943 *java/jpsgcs/alun/linkage/LinkConstants.java
7c48ad0fac4b16f5d0e1ee50e2b185ad *java/jpsgcs/alun/linkage/Linkage.java
00f8d3e5fc6807b3bb013f61575c54ec *java/jpsgcs/alun/linkage/LinkageDataSet.java
0393ce92a3112a13639d8f6a7076dd99 *java/jpsgcs/alun/linkage/LinkageException.java
794d22214260e5a1778f2f1265bd828a *java/jpsgcs/alun/linkage/LinkageFormatter.java
3b385b0007dd3a1fb6b09428dde49cbd *java/jpsgcs/alun/linkage/LinkageIndividual.java
e21ba9243a0391658c9ad9dd4a1ae1ce *java/jpsgcs/alun/linkage/LinkageInterface.java
be3e5826f63f17f3fb99a809fc22622d *java/jpsgcs/alun/linkage/LinkageLocus.java
9bcff724e0f0138a238748c6ae1c6815 *java/jpsgcs/alun/linkage/LinkageParameterData.java
55fb58849a3f90dd83d50acae057c212 *java/jpsgcs/alun/linkage/LinkagePedigreeData.java
2005769d17cd54adb368fc0620b4c4e2 *java/jpsgcs/alun/linkage/LinkagePhenotype.java
978501b327825c3372b2b7e2d01f0896 *java/jpsgcs/alun/linkage/NumberedAlleleLocus.java
1bc459d6e7545a0f9d0493a830d0fb13 *java/jpsgcs/alun/linkage/NumberedAllelePhenotype.java
5cd20804fdc42217a4e9350a25c83ea6 *java/jpsgcs/alun/linkage/QuantitativeLocus.java
00913479a064651ac5a3b640fd17a257 *java/jpsgcs/alun/linkage/QuantitativePhenotype.java
4b3f5bb85468f9af096b1f65a1cb60e7 *java/jpsgcs/alun/linkage/SteppedLinkageData.java
422d4f1cff8c4372dcdb61f550c4e359 *java/jpsgcs/alun/linkage/TransposedPedigreeData.java
d0bc1cfbc7fe0e003846137c7ff100bf *java/jpsgcs/alun/markov/DenseTable.java
0605cf9bb39ed3ffb969213cf9948045 *java/jpsgcs/alun/markov/Function.java
49f9f3680ec9c74dd55744d0e70dd0ca *java/jpsgcs/alun/markov/Functions.java
b522367bbc30949ee3499da6f9aa3dea *java/jpsgcs/alun/markov/GraphicalModel.java
1dd2e393d74eeb42645d888663d57e06 *java/jpsgcs/alun/markov/Iterable.java
6f872515dc272ab22e7f44708f73c298 *java/jpsgcs/alun/markov/MarkovRandomField.java
0f397303b6bf830495d972a37add6157 *java/jpsgcs/alun/markov/ModelInfo.java
bdc7f9d37863cad3a7045dfe408dd59d *java/jpsgcs/alun/markov/MultiVariable.java
4240166533fd8122af8ed7cab78670e5 *java/jpsgcs/alun/markov/Potential.java
a68aa58cd9c9371ccef0dfa31a868a4c *java/jpsgcs/alun/markov/Table.java
7e84570063a2a9f6d85594dc09eeaf45 *java/jpsgcs/alun/markov/Trivial.java
89e3b0f27c29c011a50eb7f6872fe5b2 *java/jpsgcs/alun/markov/Variable.java
eb74781a9b8328db003df0697b87377f *java/jpsgcs/alun/pedapps/AlleleSharing.java
475a92a09f1a48057a3a46d2f4da53b1 *java/jpsgcs/alun/pedapps/CompleteHaplotypes.java
f662654905f64c8d3b63b15452b6bf8e *java/jpsgcs/alun/pedapps/CompletingPenetrance.java
482508e785707b901693c7c083ee25db *java/jpsgcs/alun/pedapps/ErrorCount.java
94e301113b42e55e72af9e67a5e77cd9 *java/jpsgcs/alun/pedapps/GeneCounter.java
718daaee97c5181d44b696c6db6d9269 *java/jpsgcs/alun/pedapps/GeneDropper.java
0dfb80c97a31e55b37777daec159cff2 *java/jpsgcs/alun/pedapps/GeneticMap.java
21747f40d4daefbaa5d750feb99a73b2 *java/jpsgcs/alun/pedapps/Kinship.java
4e1d1aecf0261f53a62f3b5d09e90dbd *java/jpsgcs/alun/pedapps/LocInfo.java
33e0c8ce083075aabef74f7545a9b5c7 *java/jpsgcs/alun/pedapps/MarriageNodeGraph.java
c69eb8f0ae22151a842deeff494cabbf *java/jpsgcs/alun/pedapps/MultiPoints.java
01880c6820f852e4c27251604f24f5d6 *java/jpsgcs/alun/pedapps/Pedigrees.java
cb97b7443891209d6679ff94e727ede8 *java/jpsgcs/alun/pedapps/PhaseKnownHaplotypes.java
544d4ba7444124ecd1b3222814eccf10 *java/jpsgcs/alun/pedapps/TLods.java
863d0fbf7a080c71fe0dc4e577ef4535 *java/jpsgcs/alun/pedmcmc/Allele.java
d1a6e5ec0e12b46b0a29860940d27759 *java/jpsgcs/alun/pedmcmc/AlleleErrorPenetrance.java
75a9261eeb368a44a87c6344d8a6e0b6 *java/jpsgcs/alun/pedmcmc/AllelePenetrance.java
cdb445420b2e1993e0508478d59961b0 *java/jpsgcs/alun/pedmcmc/AllelePrior.java
055e1c1c10ebc10523c539f960cefc7b *java/jpsgcs/alun/pedmcmc/AlleleSegregation.java
aab3b2d925a016056b3cc91278798914 *java/jpsgcs/alun/pedmcmc/AlleleTransmission.java
6ea4edc626f58a56847df73b95e025dc *java/jpsgcs/alun/pedmcmc/AuxGraphicalModel.java
878b3afb688a078846913c0000b619a8 *java/jpsgcs/alun/pedmcmc/AuxLinkFunction.java
3dfa458d2a4341e80ef0aac4d835e6bf *java/jpsgcs/alun/pedmcmc/AuxLocusFunction.java
06ce3b507593670fb4baaa8566ef826f *java/jpsgcs/alun/pedmcmc/AuxOneGenVariable.java
6fb637e9a4c80d874091ee66eda47907 *java/jpsgcs/alun/pedmcmc/AuxThreeGenVariable.java
2a1fd121283d10b2daccb1f0304cdadf *java/jpsgcs/alun/pedmcmc/AuxVariable.java
967fb74f98c90d42743159e251b4bd53 *java/jpsgcs/alun/pedmcmc/Error.java
84cacc85f4ab9417fe3ff17852c36dc5 *java/jpsgcs/alun/pedmcmc/ErrorLocusProduct.java
53d119eb731a1e0bbd988190b6ea36ed *java/jpsgcs/alun/pedmcmc/ErrorPrior.java
7829048a3672ccb2515f11f48f32e553 *java/jpsgcs/alun/pedmcmc/ExtendedLMSampler.java
108262166d13fa1acf5db1e775531a6d *java/jpsgcs/alun/pedmcmc/GenepiFunction.java
e5e63c2e8c06b9a3c067849af8921671 *java/jpsgcs/alun/pedmcmc/Genotype.java
a22d90fd536d82e59cc6e323a6c350c7 *java/jpsgcs/alun/pedmcmc/GenotypeErrorPenetrance.java
97b07eca1e6a0c5010ccf2cd8f36e1d1 *java/jpsgcs/alun/pedmcmc/GenotypePenetrance.java
0bf3b2cb083a162da47e2c943b043cdd *java/jpsgcs/alun/pedmcmc/GenotypePrior.java
420b6165404f9d837d217650473136b6 *java/jpsgcs/alun/pedmcmc/Inheritance.java
423bd0f8b4734b5e42dd34269bb56296 *java/jpsgcs/alun/pedmcmc/LDModel.java
3bc8e2728bde2c35daa8c9de1b4748b2 *java/jpsgcs/alun/pedmcmc/LocusMeiosisSampler.java
b89c41fe09d4db5eec938d2c963b3905 *java/jpsgcs/alun/pedmcmc/LocusProduct.java
40926962cb8e698bc248ead11908ee79 *java/jpsgcs/alun/pedmcmc/LocusSampler.java
07d68b8ba8606111dd7ab9fc662243f0 *java/jpsgcs/alun/pedmcmc/Recombination.java
694b8f5df630ff19bf0ad83217267a2a *java/jpsgcs/alun/pedmcmc/TwoLocusProduct.java
c9d5654bd9d8c1f6317eb38033dd198a *java/jpsgcs/alun/pedmcmc/TwoSidedRecombination.java
feda83402d4406389ed156e400094e88 *java/jpsgcs/alun/random/AdaptiveRejection.java
fcd8c27e6f0ea775f39e88d3d703f120 *java/jpsgcs/alun/random/AhrensBinomial.java
d1bd78bca6df6333c9f43597036698eb *java/jpsgcs/alun/random/AhrensDieter.java
085a4eedd5d95434febb13a1a69d9e85 *java/jpsgcs/alun/random/AliasRejection.java
fcd7c085b8c893cc6a195054f80e9f01 *java/jpsgcs/alun/random/BernoulliRV.java
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