8e524426b837c106a866edca1be8f511 *DESCRIPTION
44449602aa1357f83cf27fad258a7318 *NAMESPACE
1b682de2c3386d5ee806be10949cf607 *NEWS.md
fde934edda9a6343c6629396025100f5 *R/Classes.R
7ccf7890a2db49d97dcd826277af731a *R/Clones.R
8f05c544ed0f11badceb87a8f5d9d993 *R/Data.R
0b748e4e92fa8b6169f72864baa28766 *R/Dowser.R
68fa21fb9429c5d90e7775387724a566 *R/Germlines.R
28f64c0b17e4347060ce637e17b88d48 *R/Plotting.R
b7279a7d55110b796510a6c44c8c050b *R/Statistics.R
99c3639e779e406a6bc56116a42fc2a1 *R/TimeTreesFunctions.R
de0a5d28458ad2bd61a20af7ad6218d1 *R/TreeFunctions.R
e137648ea17a9c23c85030c96d9b15d1 *R/zzz.R
f23ee7d2563d391bbeae9a948fa36daf *README.md
533839446f70bde34a1050627ce80586 *build/partial.rdb
ff4ff1439a9208fbed66fea587115bf2 *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
24d2b499f900c4110107a45a35ac156e *inst/doc/Building-Time-Trees-Vignette.R
4bdb7c794c439c0dc1281db5cd5521ee *inst/doc/Building-Time-Trees-Vignette.Rmd
1301abfbf4d708dbc0a9fdb6a3bd7b05 *inst/doc/Building-Time-Trees-Vignette.pdf
3b4ffd1c05c87af513f94fe5fab21e4f *inst/doc/Building-Trees-Vignette.R
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363e7317ca8ea02eed6ccccb951d972a *inst/doc/Building-Trees-Vignette.pdf
50d363da12e290c7e2e61e6e8555ae78 *inst/doc/Discrete-Trait-Vignette.R
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606d618e9a521f83b48be7b73c728ccc *inst/doc/Germlines-Vignette.R
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641d69e14ae477e3851fc814b2549a20 *inst/doc/Germlines-Vignette.pdf
e79a876360a0feaf3eb5ca4891a49e8e *inst/doc/Measurable-Evolution.R
cf2600a9ceb5b1eee7fd5360e6e58a4e *inst/doc/Measurable-Evolution.Rmd
359284791edd9d4d7f009c4fb87a2704 *inst/doc/Measurable-Evolution.pdf
6a7d2d0ce05dcde37a19323f0ee71af5 *inst/doc/NonB-Cell-Data.R
887574306dafdf6d05fbe788be034a66 *inst/doc/NonB-Cell-Data.Rmd
c9489ea37a852b848b84afc7d2c45b9e *inst/doc/NonB-Cell-Data.html
52450882bfdc435fc92e8818efc20a53 *inst/doc/Plotting-Trees-Vignette.R
cb77a28582379c8b2abfa8a4f322b06a *inst/doc/Plotting-Trees-Vignette.Rmd
fd1aa3acf8f5f326561ed01d4e6d7bce *inst/doc/Plotting-Trees-Vignette.pdf
1190ca7eba800ec4027b7c74412fb020 *inst/doc/Quickstart-Vignette.R
54c44eae92070da12f7048147c2d867f *inst/doc/Quickstart-Vignette.Rmd
222f3ea97f7d6c4688517865f9f51ae3 *inst/doc/Quickstart-Vignette.pdf
39bba22299879dec16a69b8b4b01e914 *inst/doc/Resolve-Light-Chains-Vignette.R
20db9100afea1a1f58c243ad4cc71d71 *inst/doc/Resolve-Light-Chains-Vignette.Rmd
7ae75583a0061e20499c2115b91f5440 *inst/doc/Resolve-Light-Chains-Vignette.pdf
5f724fbe84d1fe1172ff6306756cf33a *inst/doc/Sequences-Vignette.R
f866da3a01da9cd9f98a13a8c7c9b145 *inst/doc/Sequences-Vignette.Rmd
01549bcdcc6837633a291a2895bfec62 *inst/doc/Sequences-Vignette.pdf
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
07a0480a6094357dc465b926b4f5c2ab *man/TimeTrees.Rd
79e34816c2af0730611682dd2df821c2 *man/airrClone-class.Rd
23971e747faf2ea045b847dd708c3c6d *man/bootstrapTrees.Rd
d869a113690e4f4b69d15e7ec786f2ab *man/buildBeast.Rd
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b4fb901e512f9e42da2dfed4d915a34b *man/buildGermline.Rd
cc03b4a9f7f821848e5720442cf3b60c *man/buildIgphyml.Rd
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41ef679276a90097bba414655bfc3df0 *man/buildPhylo.Rd
2f3362d3e3bbf34c0c779aa4eedeab52 *man/buildPratchet.Rd
7ecb807dc193a909149656a671ab757f *man/buildRAxML.Rd
027139fb0edaccf97e4d7a7c59987e73 *man/calcRF.Rd
cec0046df0120feba2eaaa93d8601651 *man/checkDivergence.Rd
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
f714e341489bf1976e155f198a90e450 *man/create_max_height_prior.Rd
2e10c3dd4f8b957ae78898abb2c432a4 *man/create_root_freqs.Rd
da8c4a642e97b150c30a9d8e3d00e16e *man/create_starting_tree.Rd
37ef9ab897291338939971657f8c12b1 *man/create_traitset.Rd
4ca800f81fdf8adc46e004789506d4af *man/dfToFasta.Rd
a47d14d6d11a6730bc95a3935fbbab0a *man/downsampleClone.Rd
80ab5f6f4381ae042639b829c2dfaa6e *man/dowser-package.Rd
22bdaca807df84a36c059ac142d42504 *man/dowser.Rd
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8a34d081b789eda2f7a3a0b47d45afe4 *man/findSwitches.Rd
f41d9a808719a9b1c31e1217c6d690fa *man/formatClones.Rd
a04aa827a8535a7cf691630efded24fb *man/getAllSeqs.Rd
b28cf1ef2a446b3e801ca4f975972ee4 *man/getBootstraps.Rd
887b02022f0014ae68662f23842f20e9 *man/getDivergence.Rd
c234ac75f5dfc6052e83de7ee0719457 *man/getGermline.Rd
c29396ce3c2f8eb89b6aca71d23b0678 *man/getNodeSeq.Rd
a89dd136ec62ecdf3b86e00e64a49541 *man/getPalette.Rd
77a060445bb569fd6f6c8a1d0fc681fc *man/getSeq.Rd
0c99c3d0de15ab911fc2a1928a28221d *man/getSkylines.Rd
e7ca6d9671a431b79d8c1c5d5c5c3a14 *man/getSubTaxa.Rd
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37bb9de10fca769d97579f748163c092 *man/getTimeTrees.Rd
0c5630a381df94e280764a9a0de1959f *man/getTimeTreesIterate.Rd
ccfb873b589c6b15b9ceedcdc25a9fff *man/getTrees.Rd
2faabf1458b924aa8bdaf392557db50a *man/makeAirrClone.Rd
6723aeb7896e3e6944a45aa45de63918 *man/makeModelFile.Rd
3f87df117e92e6c8e0eaf351278fb410 *man/makeSkyline.Rd
dc63ed960e4d6814854ac30d9d6c71e0 *man/maskCodons.Rd
6cabb1c63b002519d18554146240e9c5 *man/maskSequences.Rd
3526e6467f678a05a1a035b315574a26 *man/plotSkylines.Rd
1846d69cd7796de09fd4a5451d0e2f5a *man/plotTrees.Rd
1984c3b25383e3bab58c8049fd1e1792 *man/readBEAST.Rd
b0aa67a16a29eab800e3b2bfb56277f7 *man/readFasta.Rd
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
adca66e2b46dfc67cef68ec02b617e8d *man/runCorrelationTest.Rd
c5984421c1ad8788e400245d98f24e0a *man/sampleCloneMultiGroup.Rd
4c94d8dacfaf7b911804f710926991e5 *man/sampleClones.Rd
cb2e435cef4d9d4e1d0ee524971cb99d *man/scaleBranches.Rd
75e49d81275a9717d99c9417d9cb01a2 *man/stitchRegions.Rd
17f878c7ee16daea4a8ecbc1c13fb9d4 *man/stitchVDJ.Rd
c1b34754dfba1817e292b4b0e19febae *man/stopCodonCheck.Rd
c20d0352f660d2779a73e29b8b7a53a4 *man/testPS.Rd
858306ab93320f278ef35c1082a1773d *man/testSC.Rd
adc0e4b9da3664e521a0b44836318e39 *man/testSP.Rd
855c4e4239f84a1384a0514f39795210 *man/treesToPDF.Rd
f04857f96eecf0d4341caf75e84c0a92 *man/writeCloneSequences.Rd
84efaf0911081f6dd11934c72614126c *man/writeLineageFile.Rd
01c5a96f073ad70ed76ceb3a1d0e484c *man/write_clone_to_xml.Rd
064dd9dee7b232f83533d3e2c9982c18 *man/write_clones_to_xmls.Rd
4bdb7c794c439c0dc1281db5cd5521ee *vignettes/Building-Time-Trees-Vignette.Rmd
29394a52ea7e6725533a3b5afb4aa621 *vignettes/Building-Time-Trees-gc-trees.png
3a336eebffaff346812d595900a1ba5b *vignettes/Building-Time-Trees-mixed-trees.png
bef3dbb099845e402c4e8da600dc5aca *vignettes/Building-Trees-Vignette.Rmd
ba585e1361b0a75b95049126b7292bc1 *vignettes/Discrete-Trait-Vignette.Rmd
dcf1c6e71cff2cc6a01dbdbe11255e7a *vignettes/Germlines-Vignette.Rmd
cf2600a9ceb5b1eee7fd5360e6e58a4e *vignettes/Measurable-Evolution.Rmd
887574306dafdf6d05fbe788be034a66 *vignettes/NonB-Cell-Data.Rmd
cb77a28582379c8b2abfa8a4f322b06a *vignettes/Plotting-Trees-Vignette.Rmd
54c44eae92070da12f7048147c2d867f *vignettes/Quickstart-Vignette.Rmd
20db9100afea1a1f58c243ad4cc71d71 *vignettes/Resolve-Light-Chains-Vignette.Rmd
f866da3a01da9cd9f98a13a8c7c9b145 *vignettes/Sequences-Vignette.Rmd
b95c88d57f7c67c97b5921d37fa4e913 *vignettes/isotype_model.txt
