4986afc45af87a0b97cdf96e964aa222 *DESCRIPTION
f07020b05a7f15390da68d12223445aa *NAMESPACE
e2d8e70b06d9ef542b310ab0b9d367fd *NEWS.md
6237a9d7da2ffe35bda73c7d0984fea4 *R/RcppExports.R
9e6e2c503b6ecfa9e86939c225d69892 *R/calculations.R
cb7aeeb2e74df9c115bc3b1b07f030ae *R/classes_methods.R
3c3f215b020b9135b56094d665be3bc2 *R/data_export.R
ed5e2610f08cc25f863924eaa82cbe66 *R/data_import.R
0d9bdc6ee67b2232e522914013a7ba2a *R/hindhe.R
8b7c58d5756a2632abd2bb237d906343 *R/overdispersion.R
e8b83a2815e7b83a03c80d58cc261e80 *R/pipelines.R
6f523696c446ef3d6fe97beef4ee49a4 *R/simulation.R
afbe4209b3bb961ba3e41cbfe79ea507 *build/partial.rdb
af11d8c4a0971b909cfd58b95d44bde5 *build/vignette.rds
7e80a03859b1e6e27857d9290df73464 *data/Msi01genes.RData
974b5d9a6d88f621d07ccfcbaf25cdfc *data/exampleRAD.RData
8dd3e2bf3f0bf7b584fb4dc9a6a18224 *data/exampleRAD_mapping.RData
ec21ea6c27eea3777a87dac20a73ac9f *inst/CITATION
1b8ef163d39ee9bbf74d64d2f50eb504 *inst/doc/isolocus_sorting.R
40c6e59908abe8c6ad2dcd7742fab978 *inst/doc/isolocus_sorting.Rmd
db2613d9768b5bcb44a0bca8262c4acf *inst/doc/isolocus_sorting.html
c46f0ebdc4bbb33641e85dc46982ee0c *inst/doc/polyRADtutorial.R
d1e7aba967cbb83ef39ada0f967612ab *inst/doc/polyRADtutorial.Rmd
705049a0265d9d706128051fe4d1417e *inst/doc/polyRADtutorial.html
90a7f3749e5a4b70066c3a481355cd33 *inst/extdata/ClareMap_HapMap.fas.txt
d06b0b7eb91371ed245c7c4810e26770 *inst/extdata/ClareMap_HapMap.hmc.txt
d1b7f7491d5395b04fe23023aa79e769 *inst/extdata/ClareMap_alignments.csv
73af2a9ea221cf0e84576500e91aed3a *inst/extdata/DArTag_BLAST_example.txt
41c289051eb17e6da74b3fc4cdf7305a *inst/extdata/DArTag_BLAST_example2.txt
3ff290160292bc5a41cbd467b2ca0810 *inst/extdata/DArTag_example.csv
a3ab981c85f8e98300db65a424e66b76 *inst/extdata/DArTag_example2.csv
196634538c7cc7cbb0dd6ecf73a4195d *inst/extdata/MsaHindHe.RData
e40d853f7f657d6001e87435836a9256 *inst/extdata/MsaHindHe0.RData
0b5a7e044d48b345d676568baa641770 *inst/extdata/MsaHindHe2.RData
b584b212bc0c0ec084cba0fb8b7a4734 *inst/extdata/MsaHindHe3.RData
a657e0dcafda950e449d6e51fa7b0356 *inst/extdata/Msi01genes.vcf
f2a3b2a92c245fb1ccfaa1859c8256c2 *inst/extdata/Msi01genes.vcf.bgz
647541d81fd0410db9830ae2927b5de8 *inst/extdata/Msi01genes.vcf.bgz.tbi
5fa21c5e19fb7af55153fadab233df81 *inst/extdata/Msi_ploidies.txt
a3132af9e1d17abb2b11229e70de62bb *inst/extdata/examplePCA.RData
a78a3ce434a1bec44e264d0a75c0ee1a *inst/extdata/exampleTASSEL_SAM.txt
46df2e9b60a7c4043f49b1ab00ceeb94 *inst/extdata/example_TagTaxaDist.txt
db2b7af7bcaf85846cfc6aeb6109cc1d *inst/extdata/simulate_rad_data.R
d744b9727f084b5373e7143b829de6d2 *inst/extdata/vcfdata.RData
e22d8d47e27f1342e2ed23616e1269e4 *inst/python/README.md
ff942a01104f7346c9a4f529a7f4c8ae *inst/python/isoloci_fun.py
265d2f7d87c5b8ddcd6711141e15f7ef *inst/python/process_isoloci.py
23619ed49a508ae8868af4d3fd66f38c *inst/python/process_sam_multi.py
1a9ea84d520c680b2ab43fa717663410 *inst/python/tassel_vcf_tags.py
08159e63fdb73a0d66068109a42257f6 *man/AddAlleleFreqByTaxa.Rd
e89614d835ed5006f5c28bb927f52efd *man/AddAlleleFreqHWE.Rd
1d42c393baa73570046dc7c90386917b *man/AddAlleleFreqMapping.Rd
93d763e114db43a37471ced013edd7e9 *man/AddAlleleLinkages.Rd
3ea9318da228f3574ba9e8755c36e2c2 *man/AddGenotypeLikelihood.Rd
c19e6c317443ed2585de5d1cf09b1eb8 *man/AddGenotypePosteriorProb.Rd
389004adb87bdb8e94a2919c2cdcc0a6 *man/AddGenotypePriorProb_ByTaxa.Rd
f204655ed14c38799a9c29b1c535ade6 *man/AddGenotypePriorProb_Even.Rd
eca8cd0906b2109597f9a7aefba1d11e *man/AddGenotypePriorProb_HWE.Rd
1afb33f350470c6135b692115acd378a *man/AddGenotypePriorProb_Mapping2Parents.Rd
a403c888b1076b229df2085c7538f7f4 *man/AddPCA.Rd
1a946cba3aed8ae2bb4d89ade4531252 *man/AddPloidyChiSq.Rd
559c095869c21d8d543c584396d31b37 *man/AddPloidyLikelihood.Rd
e31aaffb23304ce684d1723ebf4629eb *man/CanDoGetWeightedMeanGeno.Rd
a5cea907d699c4bf254438d04c019b5a *man/EstimateContaminationRate.Rd
c06c2dbc24f6b942de8e90d6271ceef5 *man/ExamineGenotype.Rd
119b7f17205bdd4df5cf01b9f89cb1f8 *man/ExpectedHindHe.Rd
6e3ad2a931bc6fdeae0587500173ec1f *man/ExportGAPIT.Rd
0d8b8d7ba223ebb0b98a6f30d3a62d7d *man/GetLikelyGen.Rd
412886998c4147c84b38303a625da0af *man/GetTaxa.Rd
0ac1a13215a2a489a2e443e645c9aaf0 *man/GetWeightedMeanGenotypes.Rd
89aab8a1b6304c51d4f94495948a0bc0 *man/HindHe.Rd
c3b76982b51781212d0fd0593189da9b *man/InbreedingFromHindHe.Rd
ed2cc5f2f5c92a1ba8ce80883cd8bfa9 *man/IterateHWE.Rd
92756fed7c0d9fba42d4e2f4f9600122 *man/LocusInfo.Rd
0f101022fc50c7ff671ca7ab003c3a11 *man/MakeTasselVcfFilter.Rd
8bf91997f84b1b94e4eeca6077eed921 *man/MergeIdenticalHaplotypes.Rd
d5916570e537c509c0f088f76d01a124 *man/MergeRareHaplotypes.Rd
eceeb1e0ffa701cd1b47c66862e6bd81 *man/MergeTaxaDepth.Rd
c92ef5c59322e75923fa857b038f508c *man/OneAllelePerMarker.Rd
8ab9b55c95f98f4c8faf5340ede2e410 *man/PipelineMapping2Parents.Rd
6e145143102b3ed5c0161dec5814f375 *man/RADdata.Rd
e97c5fdcf2f57afc02dc64a4e3b01311 *man/RADdata2VCF.Rd
76ab2cc0ebc6ca6c983cfba32deb5359 *man/SetBlankTaxa.Rd
b2a0fae61b7e68446c3692b8e53d4520 *man/StripDown.Rd
88eea21a90ab329341154554bfba9003 *man/SubsetByLocus.Rd
c02c00595848e5e1fe87b4640781fe64 *man/SubsetByPloidy.Rd
d8c6c032affb1938d06c1b9ee6e8f5de *man/SubsetByTaxon.Rd
bff859b787fa0c45ee2ada16293d0f12 *man/TestOverdispersion.Rd
d5c6426720e40d3b54c9b0d21549d6e9 *man/VCF2RADdata.Rd
830d4231b6e68c4a06d82473042cc5a0 *man/exampleRAD.Rd
0c99872de007d66332059b44304b58e9 *man/figures/logo.png
9bebd39ac81c8988cc4986b820595f83 *man/readDArTag.Rd
66a6eed7b1a26c8029f681f5551539f1 *man/readHMC.Rd
5608f6add2f0e3d335d60f23926d35e9 *man/readProcessIsoloci.Rd
8fe6f9412d9f65a6be4e50166199c240 *man/readProcessSamMulti.Rd
3bc950510cc952c18551495cd3235e47 *man/readStacks.Rd
c95758372baab4fd3989b718b96d990c *man/readTASSELGBSv2.Rd
cb50943698ddebdf05193e0304dfaa8a *man/readTagDigger.Rd
5d25e470b224b2575ae505148529ff4b *man/reverseComplement.Rd
eb4e7210b82cb185e0f95d54d842c4c2 *src/AdjustAlleleFreq.cpp
cc96e323cf2bb9da039fe0ab11c7a866 *src/BestGenos.cpp
1630ac8c75cbddebb5e224587899f17e *src/FormatStructure.cpp
61a2a755e99fea227a80eb4fea6c57e9 *src/GiniSimpson.cpp
a9f7307a631d9536a7efe75f11a7a18c *src/InitHapAssign.cpp
723340f0aa2cdeb89856584b3a291715 *src/PrepVCFexport.cpp
2fd04a0490684ee305af84cd418bc419 *src/RcppExports.cpp
3027a9672accc66a5d6f28c43883dce7 *src/SimulateGenotypes.cpp
0b8c3cac4c181b52ffded1ab19a962b1 *src/ThirdDimProd.cpp
40c6e59908abe8c6ad2dcd7742fab978 *vignettes/isolocus_sorting.Rmd
d70d90dfc9fb86df7430f09d7ea70093 *vignettes/overdispersion_inbreeding.png
d1e7aba967cbb83ef39ada0f967612ab *vignettes/polyRADtutorial.Rmd
a413b5b6e0270008a2e7791a91268559 *vignettes/subsetdata.py
