49d50d8fcade6d912a4bd2258a2efd1d *DESCRIPTION
34aaf80c4dd05069a890b16345b64e31 *NAMESPACE
8d1a1d2eb12c2178c484702e0ed32f10 *NEWS.md
fde934edda9a6343c6629396025100f5 *R/Classes.R
36b21f13d4f7e55f2cd9297e11ffadeb *R/Clones.R
8f05c544ed0f11badceb87a8f5d9d993 *R/Data.R
9553ab2f1a079528dda38d21104b24ab *R/Dowser.R
68fa21fb9429c5d90e7775387724a566 *R/Germlines.R
8119a8ab91e909ec7711707528129c43 *R/Plotting.R
8415458f39a2988aa2f2d6458685eb5d *R/Statistics.R
6c24c2482e0ec9d9b77b91ae3d4a027e *R/TimeTreesFunctions.R
26de5bbf9a4027fb31cd4b809b91b126 *R/TreeFunctions.R
e137648ea17a9c23c85030c96d9b15d1 *R/zzz.R
f23ee7d2563d391bbeae9a948fa36daf *README.md
1bf18d9c216b8d95033f0bd2fe2906b2 *build/partial.rdb
259ee916bff1b82fb38fa938dd325195 *build/vignette.rds
75f49cd3e4af6787687297764d1bdc1e *data/BiopsyTrees.rda
1faa905df572187c431c4b75d1cd9833 *data/ExampleAirr.rda
024bab035be8c6ad07b16104700bd3ef *data/ExampleAirrTyCHE.rda
b78b90401aaf61ed510e89b86d513b55 *data/ExampleClones.rda
f9dc276a0e661219b4340560d30c63a1 *data/ExampleDbChangeo.rda
bb0447c707c466158b1286009d497950 *data/ExampleMixedClones.rda
211c4708aecb5e7a00eb6c9cc1ad18f1 *data/ExampleMixedDb.rda
00ac3d7a8468830c43dd37493b0499f2 *data/IsotypeTrees.rda
2b928ff023e4061b7b26ffe986901c9d *data/TimeTrees.rda
f69fded519813ae2a25e1af2b964173e *inst/CITATION
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8b264ea4b862dd1500d9d66898727449 *inst/doc/Building-Trees-Vignette.pdf
9d7fd35b0f163badb058027c93914511 *inst/doc/Discrete-Trait-Vignette.R
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823a7987a91d9171c4857124d8e17eda *inst/doc/Discrete-Trait-Vignette.pdf
606d618e9a521f83b48be7b73c728ccc *inst/doc/Germlines-Vignette.R
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96cda7a04ed93bb94ed420a67645469a *inst/doc/Germlines-Vignette.pdf
14635696d997968bf0fd75d5cfdea77d *inst/doc/Measurable-Evolution.R
1863966841a1cc518b48ced99c844653 *inst/doc/Measurable-Evolution.Rmd
860d071ceb44b73822ae2a5ac933bbfc *inst/doc/Measurable-Evolution.pdf
54352f7c4170da1aed31877ade649234 *inst/doc/NonB-Cell-Data.R
e3f445645178921b4cae74d3ca69182a *inst/doc/NonB-Cell-Data.Rmd
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cf00631091b03af005a6140693a20d66 *inst/doc/Plotting-Trees-Vignette.Rmd
127c81ee2848696e4e3913d0a0909d6c *inst/doc/Plotting-Trees-Vignette.pdf
e4d93b6d78811bd3f3cd93e2b7253432 *inst/doc/Quickstart-Vignette.R
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7f2e8e0762a020180281747a88924486 *inst/doc/Quickstart-Vignette.pdf
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e9baf32e9cf2659ff6e0a110a6d4322a *inst/doc/Sequences-Vignette.R
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7e321e789c32c3671191e34a0410d8a5 *inst/extdata/germlines/imgt/IMGT.yaml
1c25a0dcc63f8bf7e753110c00a969aa *inst/extdata/germlines/imgt/human/vdj/imgt_human_IGHD.fasta
ddd6406f8d9b96b172aa089024d26f38 *inst/extdata/germlines/imgt/human/vdj/imgt_human_IGHJ.fasta
17c70e7a466f6ecc027a569eae3bca0a *inst/extdata/germlines/imgt/human/vdj/imgt_human_IGHV.fasta
9594940f90d2100f22a86cadbd9e4902 *man/BiopsyTrees.Rd
d808478a885e6ab9beb8d1fbf5fcaf7e *man/ExampleAirr.Rd
c2be64096c960b9c9bc22076c2dc4e23 *man/ExampleAirrTyCHE.Rd
7d24c4f008e1c13a40ff456b5896e8ce *man/ExampleClones.Rd
29541bcd301a47ae790c09a835e37915 *man/ExampleDbChangeo.Rd
42e51a2781c81120ea3bbd21cf486389 *man/ExampleMixedClones.Rd
ed2d7fb94445cd0f8a17b57d52ca91c1 *man/ExampleMixedDb.Rd
25725e56eea1af65c7c6de9fb2bbc042 *man/IsotypeTrees.Rd
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79e34816c2af0730611682dd2df821c2 *man/airrClone-class.Rd
23971e747faf2ea045b847dd708c3c6d *man/bootstrapTrees.Rd
38f39594fb0d4894ce51acf5c4b9d80d *man/buildBeast.Rd
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b4fb901e512f9e42da2dfed4d915a34b *man/buildGermline.Rd
d6f9093496128ae38337793e3a5c5dd5 *man/buildIgphyml.Rd
de3f4ecba97ce078a005cf39ba3d0382 *man/buildPML.Rd
41ef679276a90097bba414655bfc3df0 *man/buildPhylo.Rd
2f3362d3e3bbf34c0c779aa4eedeab52 *man/buildPratchet.Rd
7ecb807dc193a909149656a671ab757f *man/buildRAxML.Rd
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3f81cff6cdff3a07e7c51ecec4c28f06 *man/collapseNodes.Rd
4bb8afbb6aba1b57232d96408bf6c05c *man/colorTrees.Rd
9343e262b97a3bd0ebb982d427978f88 *man/condenseTrees.Rd
ac8645ec92edb8293b9dce4bc2fcd91d *man/correlationTest.Rd
91bb85aa1bbc711d9aa8444d50b5a4a1 *man/createGermlines.Rd
afa1f3302731d7d025dcfb7720898cd4 *man/create_MRCA_prior_germline.Rd
ab1818b093b3f33f0df392404769d369 *man/create_MRCA_prior_observed.Rd
5eb3b6e313e73ff219b483f8f3b09809 *man/create_alignment.Rd
abbce994eba4c08285205b46164d9e86 *man/create_height_prior.Rd
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2e10c3dd4f8b957ae78898abb2c432a4 *man/create_root_freqs.Rd
da8c4a642e97b150c30a9d8e3d00e16e *man/create_starting_tree.Rd
a9a23cc890d56c3ea398a36b6c758a0f *man/create_traitset.Rd
4ca800f81fdf8adc46e004789506d4af *man/dfToFasta.Rd
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80ab5f6f4381ae042639b829c2dfaa6e *man/dowser-package.Rd
22bdaca807df84a36c059ac142d42504 *man/dowser.Rd
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8a34d081b789eda2f7a3a0b47d45afe4 *man/findSwitches.Rd
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a04aa827a8535a7cf691630efded24fb *man/getAllSeqs.Rd
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887b02022f0014ae68662f23842f20e9 *man/getDivergence.Rd
c234ac75f5dfc6052e83de7ee0719457 *man/getGermline.Rd
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a89dd136ec62ecdf3b86e00e64a49541 *man/getPalette.Rd
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e7ca6d9671a431b79d8c1c5d5c5c3a14 *man/getSubTaxa.Rd
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4ef6b2106ca2da99d25a7a5b771943c7 *man/getTimeTrees.Rd
0c5630a381df94e280764a9a0de1959f *man/getTimeTreesIterate.Rd
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6723aeb7896e3e6944a45aa45de63918 *man/makeModelFile.Rd
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021e2fe759d902a65b2afabd4fb49d64 *man/maskCodons.Rd
29d85514f7cd7b8f412298998d5b830e *man/maskSequences.Rd
3526e6467f678a05a1a035b315574a26 *man/plotSkylines.Rd
aba734921eaec77005eefa8668bd52e1 *man/plotTrees.Rd
1984c3b25383e3bab58c8049fd1e1792 *man/readBEAST.Rd
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456d54fcc2996685e541905d3b9f55cd *man/readIMGT.Rd
c6e9007554529b50d4e6360a3032ee62 *man/readLineages.Rd
cd60bc42e18c4ea7b96226c37f866765 *man/readModelFile.Rd
20645ec19826d1f3ab9fe705dd521e21 *man/reconIgPhyML.Rd
885e257c68082b4d3b480bcdfe4b76dc *man/rerootTree.Rd
f25600f6b6fdfbcbd9d0a542b5a46f2c *man/resolveLightChains.Rd
9e04fd721a51bbc3c499ccce0e0e5527 *man/resolvePolytomies.Rd
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4c94d8dacfaf7b911804f710926991e5 *man/sampleClones.Rd
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17f878c7ee16daea4a8ecbc1c13fb9d4 *man/stitchVDJ.Rd
c1b34754dfba1817e292b4b0e19febae *man/stopCodonCheck.Rd
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858306ab93320f278ef35c1082a1773d *man/testSC.Rd
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855c4e4239f84a1384a0514f39795210 *man/treesToPDF.Rd
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3a336eebffaff346812d595900a1ba5b *vignettes/Building-Time-Trees-mixed-trees.png
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dcf1c6e71cff2cc6a01dbdbe11255e7a *vignettes/Germlines-Vignette.Rmd
1863966841a1cc518b48ced99c844653 *vignettes/Measurable-Evolution.Rmd
e3f445645178921b4cae74d3ca69182a *vignettes/NonB-Cell-Data.Rmd
cf00631091b03af005a6140693a20d66 *vignettes/Plotting-Trees-Vignette.Rmd
c702963b592a12ac24c320668847db24 *vignettes/Quickstart-Vignette.Rmd
caf2bacf4235f8f1d9530c9434633d58 *vignettes/Resolve-Light-Chains-Vignette.Rmd
d6d21c48550b8700f54b453b4ae5307c *vignettes/Sequences-Vignette.Rmd
b95c88d57f7c67c97b5921d37fa4e913 *vignettes/isotype_model.txt
