902851d563e3cf9a1b238d1f99bf558a *DESCRIPTION
3a53ba88eb0a79c0bad6dc479565087e *NAMESPACE
ff1ff00369e6a3134511832a1bce8400 *NEWS
dd83eff3b097d2f191b1dc4c1c5fb551 *R/RcppExports.R
e87bf472c114b6de7d9291aaf77d7800 *R/calculations.R
49f185c7de339d42e66355c057308317 *R/classes_methods.R
bffb2f33f5ab0c5fd7259947da23d63d *R/data_export.R
97982601b98563291b3d8e8d7bfdeffd *R/data_import.R
b21633c2f0e28be43e158963e2664544 *R/hindhe.R
63739c9b04a2d3ea02646e5bf86fbbd8 *R/overdispersion.R
b2e60a0b1e8eb25f9acc08ea55201fac *R/pipelines.R
163f179ea00dc7e744e6486dea2805dc *build/vignette.rds
6c98bfc9c96ec05f1a4a9ae6ae9530c9 *data/Msi01genes.RData
e001f2add9463b02530a48f46044f399 *data/exampleRAD.RData
bd4c029853fb0052b98324df21af7790 *data/exampleRAD_mapping.RData
912e5ff36d89be6f84527813f47ab69e *inst/CITATION
8218df937dd1bc603541936413097439 *inst/doc/isolocus_sorting.R
5e7e3007222d2cfe5736655569ac2993 *inst/doc/isolocus_sorting.Rmd
9d2bb18e1c333a54d56706e97062c812 *inst/doc/isolocus_sorting.html
50515431caa4bba2bffc6f9dbe57eb67 *inst/doc/polyRADtutorial.R
2509b89d3289064fe7ec322dac53998a *inst/doc/polyRADtutorial.Rmd
f01e19a117d11cf41c2b9c84fe74dd52 *inst/doc/polyRADtutorial.html
90a7f3749e5a4b70066c3a481355cd33 *inst/extdata/ClareMap_HapMap.fas.txt
d06b0b7eb91371ed245c7c4810e26770 *inst/extdata/ClareMap_HapMap.hmc.txt
d1b7f7491d5395b04fe23023aa79e769 *inst/extdata/ClareMap_alignments.csv
dcecf1771ef8d09b7e6073d0246e9bcd *inst/extdata/MsaHindHe.RData
db20fd41e3f205dc1f4a3bdf32543826 *inst/extdata/MsaHindHe2.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
e22d8d47e27f1342e2ed23616e1269e4 *inst/python/README.md
ff942a01104f7346c9a4f529a7f4c8ae *inst/python/isoloci_fun.py
f0ce1c5d6fbf2e4b19075ae86a52c06c *inst/python/process_isoloci.py
6ae33a53c30f3515e33c4cbb5c87d5d1 *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
b4cd46cb4f96da9b93489ea1457e78ff *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
a54e79b3f3d5952f7614c821a3c4020f *man/ExportGAPIT.Rd
fcda3b3ef2ba7dd85366ef6ccb965f05 *man/GetLikelyGen.Rd
01f00ca76c35bad53e15605ef5d84032 *man/GetTaxa.Rd
1ae9140508845711f86069494db0b8bf *man/GetWeightedMeanGenotypes.Rd
339e4c22b5caf399bfcac25c416a5033 *man/HindHe.Rd
634a17dbfd55866e7f6c33c50eb0becf *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
faf5823d7562c815367f1f7d1fbbe439 *man/TestOverdispersion.Rd
e729e2b3908a9a454c56a802dd11779f *man/VCF2RADdata.Rd
636cec568cace4cf8cc89c083e012d91 *man/exampleRAD.Rd
b11683de2fbd560def3b0fd5b754c8fc *man/readHMC.Rd
180067696100784508070130319bba0e *man/readProcessIsoloci.Rd
630b357d9c632eac40d8e0d686ca5d09 *man/readProcessSamMulti.Rd
2896d0af9201e78d30e5622f23a34d34 *man/readStacks.Rd
ecc55acc94154b1a08db8d026daed170 *man/readTASSELGBSv2.Rd
efded63c023f5f96e23b224f268a9942 *man/readTagDigger.Rd
eb4e7210b82cb185e0f95d54d842c4c2 *src/AdjustAlleleFreq.cpp
9ce21ad10e439c83432325dc4cc5948a *src/BestGenos.cpp
faddde29b24b5803fe9ee6624bb30537 *src/GiniSimpson.cpp
a9f7307a631d9536a7efe75f11a7a18c *src/InitHapAssign.cpp
0c34dcd517bb1cada1f263fe79c4e197 *src/PrepVCFexport.cpp
dc013bfc406573e8888e240e9deab44c *src/RcppExports.cpp
0b8c3cac4c181b52ffded1ab19a962b1 *src/ThirdDimProd.cpp
5e7e3007222d2cfe5736655569ac2993 *vignettes/isolocus_sorting.Rmd
5c36ad5b16c6920191a58c9fcc0787d3 *vignettes/isolocus_sorting.md
2509b89d3289064fe7ec322dac53998a *vignettes/polyRADtutorial.Rmd
bd8c1d736f959530931db429cd1f635c *vignettes/polyRADtutorial.md
a413b5b6e0270008a2e7791a91268559 *vignettes/subsetdata.py
