c56a4d09c478243abaa0280013ca5175 *DESCRIPTION
9c82035ee2a2f9e76e376a52c3a65a2e *NAMESPACE
cf76e537d07e839e65699139a8d8f8a0 *NEWS.md
5d30a15139e943bab5cc45607ad16717 *R/Classes.R
c148fe29ca234fb98f3da229c4dc4b42 *R/Clones.R
289e78f7e0930386a57e5991f421cbe2 *R/Data.R
546c96715da9e7d90b9504464cbb5f20 *R/Dowser.R
a3a2ab6eed8b03679aa5967b02f079e2 *R/Germlines.R
4631d67cb2ce0814e48589181a7cbb18 *R/Plotting.R
bdcf7274ee0b7f64b166cd08a9ad346f *R/Statistics.R
c8cd93162a59b02160403f4f920e9d90 *R/TreeFunctions.R
e137648ea17a9c23c85030c96d9b15d1 *R/zzz.R
c0f684ed42ea7f46ecff3d3f80e3b3ef *README.md
f61db891eb928123aba4412ca322f508 *build/partial.rdb
549808a94f4883f6e74b222555c7e17a *build/vignette.rds
75f49cd3e4af6787687297764d1bdc1e *data/BiopsyTrees.rda
1faa905df572187c431c4b75d1cd9833 *data/ExampleAirr.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
c9d83859d7f62d31a5a4b54455358202 *inst/CITATION
35ff72a4c5718adaa3f7da961b6b9718 *inst/doc/Building-Trees-Vignette.R
4c2362ce6fca555b789784d3296afa7c *inst/doc/Building-Trees-Vignette.Rmd
ea6a5ca9637e13b059bde8b1a0b3a76a *inst/doc/Building-Trees-Vignette.pdf
428a293743dcc891ab2eb41188a76527 *inst/doc/Discrete-Trait-Vignette.R
5c9e4a147277c3342f9d3725d134a1eb *inst/doc/Discrete-Trait-Vignette.Rmd
824cf373cd0bf7aa9bfdd2bb26dbb3b6 *inst/doc/Discrete-Trait-Vignette.pdf
a9b62cabe3bd73d32c6cda50ad3f75bb *inst/doc/Germlines-Vignette.R
32cf0604554f1a5501ece32f82a407a4 *inst/doc/Germlines-Vignette.Rmd
676cb6d863c13285c903edb0ed07f92a *inst/doc/Germlines-Vignette.pdf
083306cebeba95b7bb39f6e943d98cdc *inst/doc/Measurable-Evolution.R
1863966841a1cc518b48ced99c844653 *inst/doc/Measurable-Evolution.Rmd
816be4a0cd60df07607070c308626d3c *inst/doc/Measurable-Evolution.pdf
93c234097dab4f5626b5d5f4ef068aeb *inst/doc/Plotting-Trees-Vignette.R
cf00631091b03af005a6140693a20d66 *inst/doc/Plotting-Trees-Vignette.Rmd
97f0a41dd23125780a7345b90565ef1c *inst/doc/Plotting-Trees-Vignette.pdf
e4d93b6d78811bd3f3cd93e2b7253432 *inst/doc/Quickstart-Vignette.R
c702963b592a12ac24c320668847db24 *inst/doc/Quickstart-Vignette.Rmd
5d8cba97dfc9a945fddba336f0af9f40 *inst/doc/Quickstart-Vignette.pdf
7655db9715d0d2f60b7d3a8eb4ab582b *inst/doc/Resolve-Light-Chains-Vignette.R
175f688287ddabcc7a80e548b66ab467 *inst/doc/Resolve-Light-Chains-Vignette.Rmd
42f756039c17ff5023bb6a3beb483698 *inst/doc/Resolve-Light-Chains-Vignette.pdf
5f625da778c8e28ed97ae017dad3176e *inst/doc/Sequences-Vignette.R
ce6c349fc369b70eb1e913cddad83b3f *inst/doc/Sequences-Vignette.Rmd
21bb53d024ce516dbb0ad742b0ce0b0e *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
7d24c4f008e1c13a40ff456b5896e8ce *man/ExampleClones.Rd
29541bcd301a47ae790c09a835e37915 *man/ExampleDbChangeo.Rd
42e51a2781c81120ea3bbd21cf486389 *man/ExampleMixedClones.Rd
ed2d7fb94445cd0f8a17b57d52ca91c1 *man/ExampleMixedDb.Rd
25725e56eea1af65c7c6de9fb2bbc042 *man/IsotypeTrees.Rd
07a0480a6094357dc465b926b4f5c2ab *man/TimeTrees.Rd
2ba73be894c064881a2917eda3a3bfb0 *man/airrClone-class.Rd
8e8e452f8751c415cb041148051a7e62 *man/bootstrapTrees.Rd
b448155905abec00c5e46abbd328b6a0 *man/buildClonalGermline.Rd
b4fb901e512f9e42da2dfed4d915a34b *man/buildGermline.Rd
4802ff80142bc84d4177d985d3d3cbd4 *man/buildIgphyml.Rd
f1f63519df032542a0a0c1d154c7a316 *man/buildPML.Rd
db534e70780bd125d8d26b63ed5987c8 *man/buildPhylo.Rd
e814dcebfdc7dc68721f4993b8784475 *man/buildPratchet.Rd
8018f5f42dcdfd71de87b27b56198017 *man/buildRAxML.Rd
027139fb0edaccf97e4d7a7c59987e73 *man/calcRF.Rd
3f81cff6cdff3a07e7c51ecec4c28f06 *man/collapseNodes.Rd
4bb8afbb6aba1b57232d96408bf6c05c *man/colorTrees.Rd
9343e262b97a3bd0ebb982d427978f88 *man/condenseTrees.Rd
54595e5ee485a9d1017f9d01f082e655 *man/correlationTest.Rd
875150947f534c12bd532a63a71577b1 *man/createGermlines.Rd
a47d14d6d11a6730bc95a3935fbbab0a *man/downsampleClone.Rd
498c0a88ad970509265f96b8b4a0f24f *man/dowser-package.Rd
4afb9ab47253f9a3209e29f3dc6b9609 *man/dowser.Rd
cdedc728516bd687dce00123cd58d380 *man/findSwitches.Rd
d21972c8a3d239e6abc42289bbbd0f81 *man/formatClones.Rd
5d881497c53727d942b9fba1d9b41cff *man/getBootstraps.Rd
887b02022f0014ae68662f23842f20e9 *man/getDivergence.Rd
c234ac75f5dfc6052e83de7ee0719457 *man/getGermline.Rd
c29396ce3c2f8eb89b6aca71d23b0678 *man/getNodeSeq.Rd
a89dd136ec62ecdf3b86e00e64a49541 *man/getPalette.Rd
77a060445bb569fd6f6c8a1d0fc681fc *man/getSeq.Rd
e7ca6d9671a431b79d8c1c5d5c5c3a14 *man/getSubTaxa.Rd
006676d3f317ca7e1ce1480a846aae60 *man/getSubclones.Rd
60fa366668fb8b1707087dd1b5b1a16a *man/getTrees.Rd
a35afcc21c278b0c202063aefd6c9cd7 *man/makeAirrClone.Rd
6723aeb7896e3e6944a45aa45de63918 *man/makeModelFile.Rd
021e2fe759d902a65b2afabd4fb49d64 *man/maskCodons.Rd
29d85514f7cd7b8f412298998d5b830e *man/maskSequences.Rd
24df8c09f16ea506255329314db0433a *man/plotTrees.Rd
b0aa67a16a29eab800e3b2bfb56277f7 *man/readFasta.Rd
2a3b960c4dfcc2d15e23f896752365b0 *man/readIMGT.Rd
c6e9007554529b50d4e6360a3032ee62 *man/readLineages.Rd
79bd62325c8d1022633931217d82a764 *man/readModelFile.Rd
20645ec19826d1f3ab9fe705dd521e21 *man/reconIgPhyML.Rd
885e257c68082b4d3b480bcdfe4b76dc *man/rerootTree.Rd
cca2e84c57a8a4376001566a03a646c9 *man/resolveLightChains.Rd
9e04fd721a51bbc3c499ccce0e0e5527 *man/resolvePolytomies.Rd
adca66e2b46dfc67cef68ec02b617e8d *man/runCorrelationTest.Rd
cb2e435cef4d9d4e1d0ee524971cb99d *man/scaleBranches.Rd
7d8bf5d5bd266a741bb1f3c18e39df80 *man/stitchRegions.Rd
17f878c7ee16daea4a8ecbc1c13fb9d4 *man/stitchVDJ.Rd
752b66c02a405c02a7f58ab49a193ded *man/testPS.Rd
bef4654e598b0447df38b3fb5fe3293a *man/testSC.Rd
68332ebdc883c76da8a10fcb73ab5cd1 *man/testSP.Rd
855c4e4239f84a1384a0514f39795210 *man/treesToPDF.Rd
6cbd53105e0a26e430ee215dfe94d6c6 *man/writeLineageFile.Rd
4c2362ce6fca555b789784d3296afa7c *vignettes/Building-Trees-Vignette.Rmd
5c9e4a147277c3342f9d3725d134a1eb *vignettes/Discrete-Trait-Vignette.Rmd
32cf0604554f1a5501ece32f82a407a4 *vignettes/Germlines-Vignette.Rmd
1863966841a1cc518b48ced99c844653 *vignettes/Measurable-Evolution.Rmd
cf00631091b03af005a6140693a20d66 *vignettes/Plotting-Trees-Vignette.Rmd
c702963b592a12ac24c320668847db24 *vignettes/Quickstart-Vignette.Rmd
175f688287ddabcc7a80e548b66ab467 *vignettes/Resolve-Light-Chains-Vignette.Rmd
ce6c349fc369b70eb1e913cddad83b3f *vignettes/Sequences-Vignette.Rmd
b95c88d57f7c67c97b5921d37fa4e913 *vignettes/isotype_model.txt
