ae3b17605b9dd83dec076ba11dc0334c *DESCRIPTION
555cc51de75f7b1a35acaa0ca599c2db *NAMESPACE
c1cc55a861b10bb39abf5428588c0cb5 *NEWS.md
fde934edda9a6343c6629396025100f5 *R/Classes.R
9da4bcf4f839b532f0dfda7f2aabed16 *R/Clones.R
8f05c544ed0f11badceb87a8f5d9d993 *R/Data.R
a15f44ca682b0e3942a6bb302f6d928b *R/Dowser.R
91a375b74fc2071386a7a5307dbad09d *R/Germlines.R
4c73127fc31248d6cd5ac6ad1786de70 *R/IO.R
cfdf33055dae4c4f9fe759fd9c4f6f25 *R/Plotting.R
4ccd738b35cbcb8dd891d826e7891934 *R/Statistics.R
7d72522e0255d378467207ec6ee88cb1 *R/TimeTreesFunctions.R
9271c8207860abc916d976e14bcb6036 *R/TreeFunctions.R
e137648ea17a9c23c85030c96d9b15d1 *R/zzz.R
7ba8d248ed0220e62bf64c2d599c50d6 *README.md
f51ba7c8bc94d8cf1fd072b85c6e53ab *build/partial.rdb
695618eba45350f086f2e909659df2bd *build/vignette.rds
90fa52aee305a3a6ce0ffcc0f0416e2d *data/BiopsyTrees.rda
1faa905df572187c431c4b75d1cd9833 *data/ExampleAirr.rda
024bab035be8c6ad07b16104700bd3ef *data/ExampleAirrTyCHE.rda
75310978f9769e4858f236e3a9756923 *data/ExampleClones.rda
f9dc276a0e661219b4340560d30c63a1 *data/ExampleDbChangeo.rda
9b2e1eed14a1fac902cd6d862008f44b *data/ExampleMixedClones.rda
211c4708aecb5e7a00eb6c9cc1ad18f1 *data/ExampleMixedDb.rda
0d42e1dbf7d29e4c26d6ebcc476d2ed1 *data/IsotypeTrees.rda
dcb2a9a4784a6e0d967fef1450411049 *data/TimeTrees.rda
f69fded519813ae2a25e1af2b964173e *inst/CITATION
daadb1d6a418f3472316c6123c59b952 *inst/doc/Building-Time-Trees-Vignette.R
ea671b5b306770896c330b2dbd217014 *inst/doc/Building-Time-Trees-Vignette.Rmd
06975c3179c2566ca01e7a0d5dbf795b *inst/doc/Building-Time-Trees-Vignette.pdf
3b4ffd1c05c87af513f94fe5fab21e4f *inst/doc/Building-Trees-Vignette.R
bef3dbb099845e402c4e8da600dc5aca *inst/doc/Building-Trees-Vignette.Rmd
c3fa4fb0ce3ae0d3e3758c6044623232 *inst/doc/Building-Trees-Vignette.pdf
05f9e2919337ba57608f11591d194162 *inst/doc/Input-Output-Vignette.R
32dc1f9b035e3b3420f6473c18bcb584 *inst/doc/Input-Output-Vignette.Rmd
6093bd7343743421dd700ffcaef03e62 *inst/doc/Input-Output-Vignette.pdf
e98edbbb1ff6fcd51681e9946aa1d40d *inst/doc/Plotting-Trees-Vignette.R
bd78bb5cd03a1300eab86e33a21bfa52 *inst/doc/Plotting-Trees-Vignette.Rmd
2ebedec532c561ee42b6ac1abb3ae039 *inst/doc/Plotting-Trees-Vignette.pdf
4d2e2f517071a197dbc89f2bd95b6e3b *inst/doc/Quickstart-Vignette.R
7b1ba83c858533de856d35bf92a1d31d *inst/doc/Quickstart-Vignette.Rmd
9a406c659cf143a07dff37fe1d30fa35 *inst/doc/Quickstart-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
f26ef2f223c0dd628b9d0faf422dee97 *inst/get_UCA.py
9594940f90d2100f22a86cadbd9e4902 *man/BiopsyTrees.Rd
d808478a885e6ab9beb8d1fbf5fcaf7e *man/ExampleAirr.Rd
c2be64096c960b9c9bc22076c2dc4e23 *man/ExampleAirrTyCHE.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
79e34816c2af0730611682dd2df821c2 *man/airrClone-class.Rd
23971e747faf2ea045b847dd708c3c6d *man/bootstrapTrees.Rd
aba98ccdc8e3c6aa94757c3a6fa63e56 *man/buildAllClonalGermlines.Rd
24b68c813437dc72b7178b821be709b2 *man/buildBeast.Rd
b448155905abec00c5e46abbd328b6a0 *man/buildClonalGermline.Rd
b4fb901e512f9e42da2dfed4d915a34b *man/buildGermline.Rd
34b0270d01f891ac06572d608b2df913 *man/buildIgphyml.Rd
de3f4ecba97ce078a005cf39ba3d0382 *man/buildPML.Rd
41ef679276a90097bba414655bfc3df0 *man/buildPhylo.Rd
2f3362d3e3bbf34c0c779aa4eedeab52 *man/buildPratchet.Rd
7ecb807dc193a909149656a671ab757f *man/buildRAxML.Rd
f2d09dd28292a944f25a5d08b7b422ab *man/calcRF.Rd
cec0046df0120feba2eaaa93d8601651 *man/checkDivergence.Rd
f175caace95a1b29ff958b6418f8ee33 *man/checkNodeDivergences.Rd
3f81cff6cdff3a07e7c51ecec4c28f06 *man/collapseNodes.Rd
4bb8afbb6aba1b57232d96408bf6c05c *man/colorTrees.Rd
9343e262b97a3bd0ebb982d427978f88 *man/condenseTrees.Rd
ac8645ec92edb8293b9dce4bc2fcd91d *man/correlationTest.Rd
b2a7a299f212154730dfc0529615a096 *man/createAllGermlines.Rd
0aa5149a845fbc6cb0a22d3e805634ed *man/createGermlines.Rd
afa1f3302731d7d025dcfb7720898cd4 *man/create_MRCA_prior_germline.Rd
ab1818b093b3f33f0df392404769d369 *man/create_MRCA_prior_observed.Rd
5eb3b6e313e73ff219b483f8f3b09809 *man/create_alignment.Rd
abbce994eba4c08285205b46164d9e86 *man/create_height_prior.Rd
f714e341489bf1976e155f198a90e450 *man/create_max_height_prior.Rd
2e10c3dd4f8b957ae78898abb2c432a4 *man/create_root_freqs.Rd
da8c4a642e97b150c30a9d8e3d00e16e *man/create_starting_tree.Rd
37ef9ab897291338939971657f8c12b1 *man/create_traitset.Rd
71aebd9429cd60a364ce81cbbab04847 *man/dfToFasta.Rd
a47d14d6d11a6730bc95a3935fbbab0a *man/downsampleClone.Rd
0497b048887232718d2dd51cdadbd950 *man/dowser-package.Rd
22bdaca807df84a36c059ac142d42504 *man/dowser.Rd
39b703ff5e34b6aa465e510975936443 *man/dowserObjectEquivalent.Rd
2af0bf22baf4eda766ad646386976b33 *man/exportTrees.Rd
19effae126b07ad29fc0de29be6b62c6 *man/filterCombs.Rd
abca844aaaf385450eafa18355960271 *man/filterPartialSeqs.Rd
8a34d081b789eda2f7a3a0b47d45afe4 *man/findSwitches.Rd
f41d9a808719a9b1c31e1217c6d690fa *man/formatClones.Rd
a04aa827a8535a7cf691630efded24fb *man/getAllSeqs.Rd
b28cf1ef2a446b3e801ca4f975972ee4 *man/getBootstraps.Rd
322cf8122a99acea8cff5bec2c990d24 *man/getDiffPoint.Rd
65237adee7f48968bd9bda45910b8078 *man/getDiffPoints.Rd
887b02022f0014ae68662f23842f20e9 *man/getDivergence.Rd
c234ac75f5dfc6052e83de7ee0719457 *man/getGermline.Rd
b055e912330bf041c76f03c40b9938ea *man/getHeightsAndLengths.Rd
96b1cf73270877fd753ed5c4e80a010b *man/getNodeSeq.Rd
a89dd136ec62ecdf3b86e00e64a49541 *man/getPalette.Rd
77a060445bb569fd6f6c8a1d0fc681fc *man/getSeq.Rd
5ddb34d16eb3ec3082cdbd120f7c7ea0 *man/getSeqPath.Rd
bb66dd40d2721f870ca3bd8cc810fdea *man/getSkylines.Rd
71d68b953953020f492b90143bfb2d72 *man/getSubTaxa.Rd
006676d3f317ca7e1ce1480a846aae60 *man/getSubclones.Rd
37bb9de10fca769d97579f748163c092 *man/getTimeTrees.Rd
e27cab59bdb78e8e0d843b20c49e3df3 *man/getTimeTreesIterate.Rd
7b1165885c45237c6a7db564c8325a48 *man/getTrees.Rd
ad84db807b5a4cee28f865f7808c1068 *man/getTreesAndUCAs.Rd
8545d7065cff5add9f80c366c3304ebf *man/installPythonDependencies.Rd
9062859dc893c711deaf171641413d73 *man/makeAirrClone.Rd
6723aeb7896e3e6944a45aa45de63918 *man/makeModelFile.Rd
66d7345c53488a094cf8058dbec8f9ef *man/makeSkyline.Rd
490822c77175b67c2b872cdde21e777f *man/mapSubtrees.Rd
dc63ed960e4d6814854ac30d9d6c71e0 *man/maskCodons.Rd
6cabb1c63b002519d18554146240e9c5 *man/maskSequences.Rd
d07ce6bd80e12985db557c2c6a21ee07 *man/plotMSA.Rd
3526e6467f678a05a1a035b315574a26 *man/plotSkylines.Rd
143a338bdc38de7c1556ccfe61e3a9d6 *man/plotTrees.Rd
68ac7df2df9b1346475b291e9865f110 *man/readBEAST.Rd
03baf2a66d68b707907d5f07e1935d9b *man/readFasta.Rd
d6d6a662dd19a8c5798c341ac4f8d070 *man/readIMGT.Rd
c6e9007554529b50d4e6360a3032ee62 *man/readLineages.Rd
cd60bc42e18c4ea7b96226c37f866765 *man/readModelFile.Rd
f9da263f4b1ed4e58e6ee5a5bbc14c55 *man/readTreesJSON.Rd
20645ec19826d1f3ab9fe705dd521e21 *man/reconIgPhyML.Rd
885e257c68082b4d3b480bcdfe4b76dc *man/rerootTree.Rd
f25600f6b6fdfbcbd9d0a542b5a46f2c *man/resolveLightChains.Rd
9e04fd721a51bbc3c499ccce0e0e5527 *man/resolvePolytomies.Rd
adca66e2b46dfc67cef68ec02b617e8d *man/runCorrelationTest.Rd
c5984421c1ad8788e400245d98f24e0a *man/sampleCloneMultiGroup.Rd
4c94d8dacfaf7b911804f710926991e5 *man/sampleClones.Rd
cb2e435cef4d9d4e1d0ee524971cb99d *man/scaleBranches.Rd
1a5bf735525c220c05ad457c97b8b9e5 *man/setNodeDivergences.Rd
75e49d81275a9717d99c9417d9cb01a2 *man/stitchRegions.Rd
17f878c7ee16daea4a8ecbc1c13fb9d4 *man/stitchVDJ.Rd
c1b34754dfba1817e292b4b0e19febae *man/stopCodonCheck.Rd
c20d0352f660d2779a73e29b8b7a53a4 *man/testPS.Rd
858306ab93320f278ef35c1082a1773d *man/testSC.Rd
adc0e4b9da3664e521a0b44836318e39 *man/testSP.Rd
c48c7d47dd771b48f53db975ebfccf24 *man/treesEquivalent.Rd
855c4e4239f84a1384a0514f39795210 *man/treesToPDF.Rd
58127d263ab1f4cfc48d5afd3102f097 *man/writeCloneSequences.Rd
3cba7ad67ee9528df67290924fec3824 *man/writeFasta.Rd
84efaf0911081f6dd11934c72614126c *man/writeLineageFile.Rd
c009fa6be2336fe44dcc6d1cfb359016 *man/writeTreesJSON.Rd
4e5bb34255b815483b32e071384ab415 *man/write_clone_to_xml.Rd
064dd9dee7b232f83533d3e2c9982c18 *man/write_clones_to_xmls.Rd
ea671b5b306770896c330b2dbd217014 *vignettes/Building-Time-Trees-Vignette.Rmd
bef3dbb099845e402c4e8da600dc5aca *vignettes/Building-Trees-Vignette.Rmd
32dc1f9b035e3b3420f6473c18bcb584 *vignettes/Input-Output-Vignette.Rmd
bd78bb5cd03a1300eab86e33a21bfa52 *vignettes/Plotting-Trees-Vignette.Rmd
7b1ba83c858533de856d35bf92a1d31d *vignettes/Quickstart-Vignette.Rmd
