165a9bf0d0b3c30efb80979f687c11de *DESCRIPTION
89e677080c581f7da7f01856ebc930bb *NAMESPACE
05ba2360a71b186cca7f0b74be79d31b *NEWS.md
3aa923d95be8b95beadb4c54d86a9665 *R/Classes.R
498bab7ae923d9bfc1b19ccc0b3bc3b2 *R/Clones.R
141f44a4c82976c123bcaf9bff268552 *R/Data.R
441b7243ce5c4e870003ab18e73f4d4f *R/Dowser.R
28548ad3bd1ef1edacc28309d9338705 *R/Germlines.R
72bbcddfdd69bf81482679007fd31442 *R/Plotting.R
d6fbe8ca4a0c6a112f08e102283f452a *R/Statistics.R
0325798df956df043c5e510c2f819758 *R/TreeFunctions.R
96f6fca3fe3c0719633c9fe6150b5c84 *README.md
e12e37b6cb3f3648ce604337fe45cade *build/vignette.rds
ca01cdcfb5587a747072e63875863c7f *data/ExampleAirr.rda
1feace4dbc17bb3a58dfe87832b9b296 *data/ExampleClones.rda
f9dc276a0e661219b4340560d30c63a1 *data/ExampleDbChangeo.rda
361e0bdac3f7481035acb19af47f4579 *inst/CITATION
62afc56e873f919605087efb37c46d06 *inst/doc/Building-Trees-Vignette.R
f3d423485aa1382a32e72b71e48f83d3 *inst/doc/Building-Trees-Vignette.Rmd
b91c0055394a6cd0bd6a9e75738acfec *inst/doc/Building-Trees-Vignette.pdf
0da6bc626e6f51c13e03384f50aaff82 *inst/doc/Discrete-Trait-Vignette.R
abdd12496e446d2b36e4960312067535 *inst/doc/Discrete-Trait-Vignette.Rmd
e29ced44bc0cf28ab9c3de84f6cf1390 *inst/doc/Discrete-Trait-Vignette.pdf
7d6e0dd99f7ba33238b4cfbd0adda8e3 *inst/doc/Germlines-Vignette.R
ef4a3623286298352730fa724844dae1 *inst/doc/Germlines-Vignette.Rmd
993d9da1097495a2b3fb731c10814e86 *inst/doc/Germlines-Vignette.pdf
cfd3cca340bd138492f31942cc7ebefb *inst/doc/Measurable-Evolution.R
4871f419798b6dde1f55e37dd6b58d7a *inst/doc/Measurable-Evolution.Rmd
76db8eebf82b0c76e285ea5507408d4a *inst/doc/Measurable-Evolution.pdf
1d04d7e845023ead23182cfe4ff8fc5a *inst/doc/Plotting-Trees-Vignette.R
5976d47e4764627d9deb8f90332ff396 *inst/doc/Plotting-Trees-Vignette.Rmd
6b2d8d936ea99e6ff98c6f0482c633ef *inst/doc/Plotting-Trees-Vignette.pdf
891e8eeecb98bb86968623ca1417c940 *inst/doc/Quickstart-Vignette.R
723d4892cd823e36ea286323d651ee0f *inst/doc/Quickstart-Vignette.Rmd
1768af677613b9e40995f752ac843e54 *inst/doc/Quickstart-Vignette.pdf
b95dac0e359fa79c7ed27a767acb4cd7 *inst/doc/Sequences-Vignette.R
52c8556360b7b3b1d4798dc0c03d45d5 *inst/doc/Sequences-Vignette.Rmd
32af55dbe523332cb84de3f64ade6363 *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
d808478a885e6ab9beb8d1fbf5fcaf7e *man/ExampleAirr.Rd
7d24c4f008e1c13a40ff456b5896e8ce *man/ExampleClones.Rd
29541bcd301a47ae790c09a835e37915 *man/ExampleDbChangeo.Rd
525ad184c4d93dd98b1f83d5c1d233b1 *man/airrClone-class.Rd
cb442d9f4736a1837032702acf1ca8f3 *man/bootstrapTrees.Rd
ed4a393a1f6f979d092859e3539691d0 *man/buildClonalGermline.Rd
bc81d5f5b37e3a764be161bf59f9e873 *man/buildGermline.Rd
4a960264ccf24fb4ebeee88b39abad01 *man/buildIgphyml.Rd
c187c052b20b0d40a266b04e71194b25 *man/buildPML.Rd
db534e70780bd125d8d26b63ed5987c8 *man/buildPhylo.Rd
e814dcebfdc7dc68721f4993b8784475 *man/buildPratchet.Rd
3f81cff6cdff3a07e7c51ecec4c28f06 *man/collapseNodes.Rd
4bb8afbb6aba1b57232d96408bf6c05c *man/colorTrees.Rd
de11c74b87d859bcedb0aa6d28d627e8 *man/condenseTrees.Rd
54595e5ee485a9d1017f9d01f082e655 *man/correlationTest.Rd
ce4f8c9edba8f5289386ab157a80fccb *man/createGermlines.Rd
a47d14d6d11a6730bc95a3935fbbab0a *man/downsampleClone.Rd
deb00b25f55432aa160700c42b0cbbdc *man/dowser.Rd
79f08feb67937314726b2c79487ce9b0 *man/findSwitches.Rd
ea144e18dfc0ed914f91af7238d98b48 *man/formatClones.Rd
887b02022f0014ae68662f23842f20e9 *man/getDivergence.Rd
07653effcfd2532eab2028793516166f *man/getGermline.Rd
c29396ce3c2f8eb89b6aca71d23b0678 *man/getNodeSeq.Rd
9f036b029ab26329b2def39bbff4ccef *man/getPalette.Rd
ea8315437b06f77e7ed1c4c6cab31a54 *man/getSeq.Rd
d98aa6bba22d5a15cd4ed8429cc3b0db *man/getSubclones.Rd
d2a0284639b5f67b6ce28d0dac9bd0ec *man/getTrees.Rd
e421ebddf971275d94a3f7da2066ecec *man/makeAirrClone.Rd
0e0f5a21052b46fad387b2c01bc0505c *man/makeModelFile.Rd
245cef5bee049db85a67924771d10360 *man/maskCodons.Rd
29d85514f7cd7b8f412298998d5b830e *man/maskSequences.Rd
072305f5a2429296a176ad88ac8b2d3e *man/plotTrees.Rd
b0aa67a16a29eab800e3b2bfb56277f7 *man/readFasta.Rd
32f4da78d443cf7effcc62971a43c6ec *man/readIMGT.Rd
d30d1f989726415c6ae66a76ad0aa853 *man/readLineages.Rd
79bd62325c8d1022633931217d82a764 *man/readModelFile.Rd
5d84a40c8c857e77e0a569ed4f5b3d84 *man/reconIgPhyML.Rd
f2d212f1c881953f3ac5b0c683b42b38 *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
d9f1798548993ce2140ad28dbe3c370d *man/testSC.Rd
bbab6444ddcc11e72466243e36fe069d *man/testSP.Rd
855c4e4239f84a1384a0514f39795210 *man/treesToPDF.Rd
6cbd53105e0a26e430ee215dfe94d6c6 *man/writeLineageFile.Rd
f3d423485aa1382a32e72b71e48f83d3 *vignettes/Building-Trees-Vignette.Rmd
abdd12496e446d2b36e4960312067535 *vignettes/Discrete-Trait-Vignette.Rmd
ef4a3623286298352730fa724844dae1 *vignettes/Germlines-Vignette.Rmd
4871f419798b6dde1f55e37dd6b58d7a *vignettes/Measurable-Evolution.Rmd
5976d47e4764627d9deb8f90332ff396 *vignettes/Plotting-Trees-Vignette.Rmd
723d4892cd823e36ea286323d651ee0f *vignettes/Quickstart-Vignette.Rmd
52c8556360b7b3b1d4798dc0c03d45d5 *vignettes/Sequences-Vignette.Rmd
