bd55dc2827b352a6bc844d666a15a279 *DESCRIPTION
c87b453c4781bc53a9df2829dc81c0db *NAMESPACE
fb5afab8519156ee5c1f73c4c13a1417 *NEWS.md
5d30a15139e943bab5cc45607ad16717 *R/Classes.R
188cf13eee17a35f6ab7bf97928211cc *R/Clones.R
ead4db41e80ffb73ae684cd051365a2c *R/Data.R
e95e4125e2df6eaf3bbf01f5082622a3 *R/Dowser.R
46a4cd2fb0762053d1b3bbd76ce2a21b *R/Germlines.R
aef9c554b89bf63304cc533d46ee138b *R/Plotting.R
f90af1068b77ac138100c353a23feb1c *R/Statistics.R
6ca638da40a7f40948af69053532f886 *R/TreeFunctions.R
e137648ea17a9c23c85030c96d9b15d1 *R/zzz.R
1db20a51f697dafc323fb17e7c198d43 *README.md
8df85135ca97a790a7e3b0f674bf365f *build/vignette.rds
75f49cd3e4af6787687297764d1bdc1e *data/BiopsyTrees.rda
1faa905df572187c431c4b75d1cd9833 *data/ExampleAirr.rda
b78b90401aaf61ed510e89b86d513b55 *data/ExampleClones.rda
f9dc276a0e661219b4340560d30c63a1 *data/ExampleDbChangeo.rda
00ac3d7a8468830c43dd37493b0499f2 *data/IsotypeTrees.rda
2b928ff023e4061b7b26ffe986901c9d *data/TimeTrees.rda
c9d83859d7f62d31a5a4b54455358202 *inst/CITATION
62afc56e873f919605087efb37c46d06 *inst/doc/Building-Trees-Vignette.R
471b216b8b9b5b0e0aa22d6d482406e9 *inst/doc/Building-Trees-Vignette.Rmd
34e27b7b1935da1b69c854671cd6cc53 *inst/doc/Building-Trees-Vignette.pdf
e7004c97606de0d3d742c15292dba3e4 *inst/doc/Discrete-Trait-Vignette.R
4e9a6fe6facaa9d1883f46e4239083e1 *inst/doc/Discrete-Trait-Vignette.Rmd
978839354d4bea207c35617e70b98441 *inst/doc/Discrete-Trait-Vignette.pdf
7d6e0dd99f7ba33238b4cfbd0adda8e3 *inst/doc/Germlines-Vignette.R
dea9718015bbda10dc48c8b9851d5568 *inst/doc/Germlines-Vignette.Rmd
d5aa6d1e3b24ae76b1adc7d10fb24a6d *inst/doc/Germlines-Vignette.pdf
70d18c8a252d2866f5a3ccaf1f0c6098 *inst/doc/Measurable-Evolution.R
1863966841a1cc518b48ced99c844653 *inst/doc/Measurable-Evolution.Rmd
e2e2a3c2c7cdb96a3a85de9693fb7d67 *inst/doc/Measurable-Evolution.pdf
b1f59191f57c506bebead33da695b7fd *inst/doc/Plotting-Trees-Vignette.R
1ba4e0630bb4c10e32ab188dc2da4c83 *inst/doc/Plotting-Trees-Vignette.Rmd
acd734065f62bddf955430f5aecc4cad *inst/doc/Plotting-Trees-Vignette.pdf
33369adf2a02a52feaa6e0f07d39d8ee *inst/doc/Quickstart-Vignette.R
d15e605d4b3ce7e8042902d476603158 *inst/doc/Quickstart-Vignette.Rmd
a3106e5f7bc798616bd5439bcd8305bc *inst/doc/Quickstart-Vignette.pdf
b95dac0e359fa79c7ed27a767acb4cd7 *inst/doc/Sequences-Vignette.R
ce6c349fc369b70eb1e913cddad83b3f *inst/doc/Sequences-Vignette.Rmd
acfb2d45be859c73f57a77253fb80296 *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
25725e56eea1af65c7c6de9fb2bbc042 *man/IsotypeTrees.Rd
07a0480a6094357dc465b926b4f5c2ab *man/TimeTrees.Rd
2ba73be894c064881a2917eda3a3bfb0 *man/airrClone-class.Rd
cb442d9f4736a1837032702acf1ca8f3 *man/bootstrapTrees.Rd
b448155905abec00c5e46abbd328b6a0 *man/buildClonalGermline.Rd
b4fb901e512f9e42da2dfed4d915a34b *man/buildGermline.Rd
9621b60cdef01b8c0016d4457f11de47 *man/buildIgphyml.Rd
f1f63519df032542a0a0c1d154c7a316 *man/buildPML.Rd
db534e70780bd125d8d26b63ed5987c8 *man/buildPhylo.Rd
e814dcebfdc7dc68721f4993b8784475 *man/buildPratchet.Rd
b97fa4aa0747352d13e2b9aaceda9b7b *man/buildRAxML.Rd
c7756435e3f72592c384e01e38af9831 *man/calcRF.Rd
3f81cff6cdff3a07e7c51ecec4c28f06 *man/collapseNodes.Rd
4bb8afbb6aba1b57232d96408bf6c05c *man/colorTrees.Rd
de11c74b87d859bcedb0aa6d28d627e8 *man/condenseTrees.Rd
54595e5ee485a9d1017f9d01f082e655 *man/correlationTest.Rd
875150947f534c12bd532a63a71577b1 *man/createGermlines.Rd
a47d14d6d11a6730bc95a3935fbbab0a *man/downsampleClone.Rd
1dd7fdc3b4f96b7a7cc15095cf07ef7a *man/dowser.Rd
1179870a6158a90a7fcc1184ddcb62a3 *man/findSwitches.Rd
c4f3980123f65e845cd2ad9f9cb627d8 *man/formatClones.Rd
5d881497c53727d942b9fba1d9b41cff *man/getBootstraps.Rd
887b02022f0014ae68662f23842f20e9 *man/getDivergence.Rd
c234ac75f5dfc6052e83de7ee0719457 *man/getGermline.Rd
c29396ce3c2f8eb89b6aca71d23b0678 *man/getNodeSeq.Rd
9f036b029ab26329b2def39bbff4ccef *man/getPalette.Rd
77a060445bb569fd6f6c8a1d0fc681fc *man/getSeq.Rd
e7ca6d9671a431b79d8c1c5d5c5c3a14 *man/getSubTaxa.Rd
d98aa6bba22d5a15cd4ed8429cc3b0db *man/getSubclones.Rd
23a33c5d1ab37db079308ebe615eac8d *man/getTrees.Rd
e421ebddf971275d94a3f7da2066ecec *man/makeAirrClone.Rd
6723aeb7896e3e6944a45aa45de63918 *man/makeModelFile.Rd
245cef5bee049db85a67924771d10360 *man/maskCodons.Rd
29d85514f7cd7b8f412298998d5b830e *man/maskSequences.Rd
8a4690949ca1fc03bbd49055448b8902 *man/plotTrees.Rd
b0aa67a16a29eab800e3b2bfb56277f7 *man/readFasta.Rd
2a3b960c4dfcc2d15e23f896752365b0 *man/readIMGT.Rd
d30d1f989726415c6ae66a76ad0aa853 *man/readLineages.Rd
79bd62325c8d1022633931217d82a764 *man/readModelFile.Rd
5d84a40c8c857e77e0a569ed4f5b3d84 *man/reconIgPhyML.Rd
885e257c68082b4d3b480bcdfe4b76dc *man/rerootTree.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
471b216b8b9b5b0e0aa22d6d482406e9 *vignettes/Building-Trees-Vignette.Rmd
4e9a6fe6facaa9d1883f46e4239083e1 *vignettes/Discrete-Trait-Vignette.Rmd
dea9718015bbda10dc48c8b9851d5568 *vignettes/Germlines-Vignette.Rmd
1863966841a1cc518b48ced99c844653 *vignettes/Measurable-Evolution.Rmd
1ba4e0630bb4c10e32ab188dc2da4c83 *vignettes/Plotting-Trees-Vignette.Rmd
d15e605d4b3ce7e8042902d476603158 *vignettes/Quickstart-Vignette.Rmd
ce6c349fc369b70eb1e913cddad83b3f *vignettes/Sequences-Vignette.Rmd
