03ae0fcf68c98b74c9dd3d957c6d047e *DESCRIPTION
9c82035ee2a2f9e76e376a52c3a65a2e *NAMESPACE
db98be539e371fbdd7455860ab849325 *NEWS.md
5d30a15139e943bab5cc45607ad16717 *R/Classes.R
92d6d9bf8e6e27721c7bbe9d23bafccb *R/Clones.R
289e78f7e0930386a57e5991f421cbe2 *R/Data.R
0ff3749e2d842a82b89820027f8d8ae4 *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
072e37206597f0c2f729ba97dad9f41e *build/partial.rdb
26290b4699d1de8ee53b1a88f22bf468 *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
d0c1f59f931994d487d420f028c3b825 *inst/doc/Building-Trees-Vignette.R
4c2362ce6fca555b789784d3296afa7c *inst/doc/Building-Trees-Vignette.Rmd
b5e99d1ea934bfd1980007d43c87d6e3 *inst/doc/Building-Trees-Vignette.pdf
799b13db264d66f2f4d9c57c5c4e2db2 *inst/doc/Discrete-Trait-Vignette.R
5c9e4a147277c3342f9d3725d134a1eb *inst/doc/Discrete-Trait-Vignette.Rmd
bf961422910c5450c46d90bc0f89e728 *inst/doc/Discrete-Trait-Vignette.pdf
7d6e0dd99f7ba33238b4cfbd0adda8e3 *inst/doc/Germlines-Vignette.R
32cf0604554f1a5501ece32f82a407a4 *inst/doc/Germlines-Vignette.Rmd
8bb5a9600e72fb40f4be576c9d2ab83b *inst/doc/Germlines-Vignette.pdf
70d18c8a252d2866f5a3ccaf1f0c6098 *inst/doc/Measurable-Evolution.R
1863966841a1cc518b48ced99c844653 *inst/doc/Measurable-Evolution.Rmd
76b3ddd9dccd836e21e79b83baf48e4a *inst/doc/Measurable-Evolution.pdf
667d76f39c92ac65bcc95acbf0179589 *inst/doc/Plotting-Trees-Vignette.R
cf00631091b03af005a6140693a20d66 *inst/doc/Plotting-Trees-Vignette.Rmd
e27784f34c1518725792f3238b311345 *inst/doc/Plotting-Trees-Vignette.pdf
6430ae1f83560fa68889eaad89b3b075 *inst/doc/Quickstart-Vignette.R
c702963b592a12ac24c320668847db24 *inst/doc/Quickstart-Vignette.Rmd
a5db5aa7ba922c04c5c8f2970b53abd8 *inst/doc/Quickstart-Vignette.pdf
47c8c33f56ee6697f5b6daea5b2e996b *inst/doc/Resolve-Light-Chains-Vignette.R
175f688287ddabcc7a80e548b66ab467 *inst/doc/Resolve-Light-Chains-Vignette.Rmd
693c6bc3090600fc174777978be0d9e9 *inst/doc/Resolve-Light-Chains-Vignette.pdf
b95dac0e359fa79c7ed27a767acb4cd7 *inst/doc/Sequences-Vignette.R
ce6c349fc369b70eb1e913cddad83b3f *inst/doc/Sequences-Vignette.Rmd
fb596f4dcee07254dccaa86de7e7e2b2 *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
7a883f6e730ce2c143b271b215d8041b *man/dowser-package.Rd
1dd7fdc3b4f96b7a7cc15095cf07ef7a *man/dowser.Rd
cdedc728516bd687dce00123cd58d380 *man/findSwitches.Rd
75c30d40730fa7005700971b759c5bcb *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
245cef5bee049db85a67924771d10360 *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
