3c03b2aab94a886879f7ef89c57ada7f *DESCRIPTION
4785c72350d56170766b8413a2133b4a *NAMESPACE
fc316d611a7beceb3e697c83ede7ca3e *NEWS.md
3aa923d95be8b95beadb4c54d86a9665 *R/Classes.R
a37d46d41faa1fe5c67348939ad110b3 *R/Clones.R
141f44a4c82976c123bcaf9bff268552 *R/Data.R
d5f89ea5bc9f3cdb26b02a7ab0dcfe01 *R/Dowser.R
d57136ae2227b028adc9fe28145dcab9 *R/Germlines.R
c2d5d00b2ca6ac7061efbd95aad2f271 *R/Plotting.R
877cb598c6b9aa189859ea57b877e110 *R/Statistics.R
f85879498d6a1892394aedd861de6a94 *R/TreeFunctions.R
2e3056749a1eeb089d422c96ab49a8b7 *README.md
962f16afdf712aee39d95be77254304b *build/vignette.rds
487420ffa0759ad2e3f70360850ec00d *data/ExampleAirr.rda
7ddc7b656ab6b73a64f68782c1cbd7b1 *data/ExampleClones.rda
f9dc276a0e661219b4340560d30c63a1 *data/ExampleDbChangeo.rda
361e0bdac3f7481035acb19af47f4579 *inst/CITATION
62afc56e873f919605087efb37c46d06 *inst/doc/Building-Trees-Vignette.R
f9bfaa045dbddb11266b8cc5e1e786f7 *inst/doc/Building-Trees-Vignette.Rmd
2750a893244248fbb5d00563eaa46da7 *inst/doc/Building-Trees-Vignette.pdf
7d6e0dd99f7ba33238b4cfbd0adda8e3 *inst/doc/Germlines-Vignette.R
8308a8869a5528c775412fc732f5ee59 *inst/doc/Germlines-Vignette.Rmd
c6ad2f9b8b5eb0fb051754070521a96b *inst/doc/Germlines-Vignette.pdf
1d04d7e845023ead23182cfe4ff8fc5a *inst/doc/Plotting-Trees-Vignette.R
d38c3f21cc376eb3ef2146250afd64c6 *inst/doc/Plotting-Trees-Vignette.Rmd
bc9276e3c058cfffc8517a1379b9a45d *inst/doc/Plotting-Trees-Vignette.pdf
767f59a65650af3353c0b4739dd1824f *inst/doc/Quickstart-Vignette.R
23568f020043d9f17236b7e86c00be2d *inst/doc/Quickstart-Vignette.Rmd
ab549c45e51d9d512a715963fc55d6df *inst/doc/Quickstart-Vignette.pdf
60f72efdc963134527e9acd7cb435725 *inst/doc/Sequences-Vignette.R
2ee83929878275fa50ec6e2fa8b9f206 *inst/doc/Sequences-Vignette.Rmd
b3f5e493de26e5f6d0b0f06b29dc060b *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
5be6db164ad75b3671d7e53c781761b3 *man/bootstrapTrees.Rd
ed4a393a1f6f979d092859e3539691d0 *man/buildClonalGermline.Rd
bc81d5f5b37e3a764be161bf59f9e873 *man/buildGermline.Rd
4a960264ccf24fb4ebeee88b39abad01 *man/buildIgphyml.Rd
6b9ec9420bfcc1e5c0c8a28be73d56d2 *man/buildPML.Rd
db534e70780bd125d8d26b63ed5987c8 *man/buildPhylo.Rd
e814dcebfdc7dc68721f4993b8784475 *man/buildPratchet.Rd
3f81cff6cdff3a07e7c51ecec4c28f06 *man/collapseNodes.Rd
4bb8afbb6aba1b57232d96408bf6c05c *man/colorTrees.Rd
de11c74b87d859bcedb0aa6d28d627e8 *man/condenseTrees.Rd
054f9f5da062a06878821839b4ef035e *man/correlationTest.Rd
e0000a4f805d17d3b08424ad7f829a8e *man/createGermlines.Rd
a47d14d6d11a6730bc95a3935fbbab0a *man/downsampleClone.Rd
8ad340135a97cfd98f76f86cadafcdd9 *man/dowser.Rd
c53a273b92edd0a4c6518b9f3703a7b5 *man/formatClones.Rd
f1e719ecef5124bad43dbf1a619416b1 *man/getDivergence.Rd
07653effcfd2532eab2028793516166f *man/getGermline.Rd
9f036b029ab26329b2def39bbff4ccef *man/getPalette.Rd
8fe17c7cdd7a669df22d8f562cfacb46 *man/getSeq.Rd
82dafb2c59fa026ecd7890c4dc7c04a9 *man/getSubclones.Rd
b336489f3c94c1319a2a432bf4433eac *man/getTrees.Rd
e421ebddf971275d94a3f7da2066ecec *man/makeAirrClone.Rd
10c2579f22bf284bfc292d007d974de4 *man/makeModelFile.Rd
245cef5bee049db85a67924771d10360 *man/maskCodons.Rd
29d85514f7cd7b8f412298998d5b830e *man/maskSequences.Rd
21aff32c95bf087ab9215f66fdb86f9b *man/plotTrees.Rd
b0aa67a16a29eab800e3b2bfb56277f7 *man/readFasta.Rd
32f4da78d443cf7effcc62971a43c6ec *man/readIMGT.Rd
d30d1f989726415c6ae66a76ad0aa853 *man/readLineages.Rd
afb0973fbdfa7dca957c92830a1b914c *man/readModelFile.Rd
6bdf7cbe20470348444c7f43394d4492 *man/rerootTree.Rd
9e04fd721a51bbc3c499ccce0e0e5527 *man/resolvePolytomies.Rd
adca66e2b46dfc67cef68ec02b617e8d *man/runCorrelationTest.Rd
cb2e435cef4d9d4e1d0ee524971cb99d *man/scaleBranches.Rd
7d8bf5d5bd266a741bb1f3c18e39df80 *man/stitchRegions.Rd
17f878c7ee16daea4a8ecbc1c13fb9d4 *man/stitchVDJ.Rd
4f3f7e3830c3054a97bfff3e90e2757d *man/testPS.Rd
4bf925e30fbbafe001df1563e1620b5c *man/testSC.Rd
d6ce282cd64e6c3f895854af21ce9cba *man/testSP.Rd
0c0b297ee7aa869c682aba7f2fc7768e *man/treesToPDF.Rd
6cbd53105e0a26e430ee215dfe94d6c6 *man/writeLineageFile.Rd
f9bfaa045dbddb11266b8cc5e1e786f7 *vignettes/Building-Trees-Vignette.Rmd
8308a8869a5528c775412fc732f5ee59 *vignettes/Germlines-Vignette.Rmd
d38c3f21cc376eb3ef2146250afd64c6 *vignettes/Plotting-Trees-Vignette.Rmd
23568f020043d9f17236b7e86c00be2d *vignettes/Quickstart-Vignette.Rmd
2ee83929878275fa50ec6e2fa8b9f206 *vignettes/Sequences-Vignette.Rmd
