912a61bd2032320a7c32a8e4033223d7 *DESCRIPTION
f6becdcdb9d0a2d6bd22c8a739446ea8 *NAMESPACE
1869b77d2c296155aafa9c18a5703382 *NEWS
8123c379ca09a99b4943922c154caa6c *R/RcppExports.R
a7c973fb43bd006b27785d294fbaccea *R/calculations.R
36fb1af98efdab682e2c30b550295ca1 *R/classes_methods.R
ab366d145a1ff00866ba8286262a317b *R/data_export.R
d8b629769693b33975a6d9414f22acb8 *R/data_import.R
e9ce3bea87b8a01faa7ce8813edebfe6 *R/hindhe.R
f6af2310b36302a804106b89118e1661 *R/overdispersion.R
b2e60a0b1e8eb25f9acc08ea55201fac *R/pipelines.R
63b6e723d71e0cdcb435957a032719e9 *R/simulation.R
adeddc43e9554178a44ae8cde1460278 *build/partial.rdb
7f0bd39b0118dd347ba0d98d6c0dd394 *build/vignette.rds
6c98bfc9c96ec05f1a4a9ae6ae9530c9 *data/Msi01genes.RData
e001f2add9463b02530a48f46044f399 *data/exampleRAD.RData
bd4c029853fb0052b98324df21af7790 *data/exampleRAD_mapping.RData
912e5ff36d89be6f84527813f47ab69e *inst/CITATION
1b8ef163d39ee9bbf74d64d2f50eb504 *inst/doc/isolocus_sorting.R
6b33cabb22f06dc3e752156624b7da69 *inst/doc/isolocus_sorting.Rmd
5682514f48b442eec75dde89ef719b3b *inst/doc/isolocus_sorting.html
ee810454486bc0064473c8877500468b *inst/doc/polyRADtutorial.R
5e6616aa9b30409b1eea182de0f525eb *inst/doc/polyRADtutorial.Rmd
69c05d72d47271fead920f8b5d689269 *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
3ff290160292bc5a41cbd467b2ca0810 *inst/extdata/DArTag_example.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
a3132af9e1d17abb2b11229e70de62bb *inst/extdata/examplePCA.RData
a78a3ce434a1bec44e264d0a75c0ee1a *inst/extdata/exampleTASSEL_SAM.txt
46df2e9b60a7c4043f49b1ab00ceeb94 *inst/extdata/example_TagTaxaDist.txt
b4b8fbdd2a8576d6cdf097580ba69f53 *inst/extdata/simulate_rad_data.R
28adb96c2fb0ba8cac6a78f33c54c3b9 *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
e603e5664bed62da0aa681b048797b66 *man/AddAlleleLinkages.Rd
87aa4284adf19b827bc05931eb012068 *man/AddGenotypeLikelihood.Rd
aa4160f278dd9bef01ffa54c85a4220a *man/AddGenotypePosteriorProb.Rd
f730f5a25daed70fae1818e52f624d39 *man/AddGenotypePriorProb_ByTaxa.Rd
98cc4a2225715c8c400c00c6c7996165 *man/AddGenotypePriorProb_Even.Rd
3a974d0277083ce7fa63e362d44bb65e *man/AddGenotypePriorProb_HWE.Rd
fd22529c23742ca806fccd8069ca009a *man/AddGenotypePriorProb_Mapping2Parents.Rd
a403c888b1076b229df2085c7538f7f4 *man/AddPCA.Rd
c9188c7459c006d764d34f908745a069 *man/AddPloidyChiSq.Rd
559c095869c21d8d543c584396d31b37 *man/AddPloidyLikelihood.Rd
49a38b514b53975ee0cf5a5465bb71de *man/AddPriorTimesLikelihood.Rd
e31aaffb23304ce684d1723ebf4629eb *man/CanDoGetWeightedMeanGeno.Rd
a5cea907d699c4bf254438d04c019b5a *man/EstimateContaminationRate.Rd
a1d767ffc4b6e1ba376de470d16fdf94 *man/ExpectedHindHe.Rd
0d17c9baf48a86d6c33adbfa1ede2bac *man/ExportGAPIT.Rd
fcda3b3ef2ba7dd85366ef6ccb965f05 *man/GetLikelyGen.Rd
01f00ca76c35bad53e15605ef5d84032 *man/GetTaxa.Rd
c0135d752cd304dad4a48f761fe85efe *man/GetWeightedMeanGenotypes.Rd
af3f2a0aed980e6a04a417d344040d4f *man/HindHe.Rd
c3b76982b51781212d0fd0593189da9b *man/InbreedingFromHindHe.Rd
d52ca5fad1e3b404d17c668af8a59b65 *man/IterateHWE.Rd
92756fed7c0d9fba42d4e2f4f9600122 *man/LocusInfo.Rd
0f101022fc50c7ff671ca7ab003c3a11 *man/MakeTasselVcfFilter.Rd
e7ab883be9919d54ee83e6724ff2cd4a *man/MergeIdenticalHaplotypes.Rd
1da0300fa0c4fc661cf59f1ea7743212 *man/MergeRareHaplotypes.Rd
eceeb1e0ffa701cd1b47c66862e6bd81 *man/MergeTaxaDepth.Rd
c92ef5c59322e75923fa857b038f508c *man/OneAllelePerMarker.Rd
279adc251036f979847cbd17162af3c2 *man/PipelineMapping2Parents.Rd
5b1a1a38f8a0e34da2a82c20b4e9f4e0 *man/RADdata.Rd
e97c5fdcf2f57afc02dc64a4e3b01311 *man/RADdata2VCF.Rd
76ab2cc0ebc6ca6c983cfba32deb5359 *man/SetBlankTaxa.Rd
628b676668d278301f1247299dd9103a *man/StripDown.Rd
88eea21a90ab329341154554bfba9003 *man/SubsetByLocus.Rd
b536743c5f9693d75652f6c34a3368fe *man/SubsetByPloidy.Rd
d8c6c032affb1938d06c1b9ee6e8f5de *man/SubsetByTaxon.Rd
bff859b787fa0c45ee2ada16293d0f12 *man/TestOverdispersion.Rd
8b2c4fc9ccbb954f76f68890fcd261cb *man/VCF2RADdata.Rd
636cec568cace4cf8cc89c083e012d91 *man/exampleRAD.Rd
0c99872de007d66332059b44304b58e9 *man/figures/logo.png
041b6e9e28aefb23c3e97ed04146700f *man/readDArTag.Rd
d81bd7dd08de537b24bcea29825ff479 *man/readHMC.Rd
180067696100784508070130319bba0e *man/readProcessIsoloci.Rd
630b357d9c632eac40d8e0d686ca5d09 *man/readProcessSamMulti.Rd
71835c9ecf021dbe882bb12a633836e7 *man/readStacks.Rd
28216e422aab811b69ae0c35bd8a57e8 *man/readTASSELGBSv2.Rd
e3d760ffadd78bcc060cf2cb2e37276f *man/readTagDigger.Rd
5d25e470b224b2575ae505148529ff4b *man/reverseComplement.Rd
eb4e7210b82cb185e0f95d54d842c4c2 *src/AdjustAlleleFreq.cpp
9ce21ad10e439c83432325dc4cc5948a *src/BestGenos.cpp
1630ac8c75cbddebb5e224587899f17e *src/FormatStructure.cpp
faddde29b24b5803fe9ee6624bb30537 *src/GiniSimpson.cpp
a9f7307a631d9536a7efe75f11a7a18c *src/InitHapAssign.cpp
0c34dcd517bb1cada1f263fe79c4e197 *src/PrepVCFexport.cpp
4eef01c8cd37edd106905daaaac9b209 *src/RcppExports.cpp
23fe2a6603215878c128e5f21fa9963e *src/SimulateGenotypes.cpp
0b8c3cac4c181b52ffded1ab19a962b1 *src/ThirdDimProd.cpp
6b33cabb22f06dc3e752156624b7da69 *vignettes/isolocus_sorting.Rmd
d70d90dfc9fb86df7430f09d7ea70093 *vignettes/overdispersion_inbreeding.png
5e6616aa9b30409b1eea182de0f525eb *vignettes/polyRADtutorial.Rmd
a413b5b6e0270008a2e7791a91268559 *vignettes/subsetdata.py
