ae3c5eae9213b0a0384dfead4bd5ea39 *DESCRIPTION
27ddda8bcebef29a7603d0f808403721 *NAMESPACE
65b306f54104f4c9da7ceb10029e74c1 *NEWS.md
32637d167ac6adde57cd25d5f272fdf9 *R/Alakazam.R
9bacdbf9fdf6b34d796247445fa65050 *R/AminoAcids.R
e05a50654991d8d4f3cae1e7756c4e9e *R/Classes.R
10df35c4b1f227a7390ea4098958418e *R/Core.R
f4a71b840d1896ce67d2db391e462fe1 *R/Data.R
f19226bba3940267805ebd3e78802a26 *R/Diversity.R
84fa4fe23d8c5e29ed1b31540b0839ab *R/Gene.R
b0fdcdba439868639deede6698a7c404 *R/Lineage.R
6ba5639ea230c7ddbf6182fc6f5e7f7c *R/RcppExports.R
cb32dad9deecf60eed6c4026931263b8 *R/Sequence.R
af167a4fb5ea6f320153ec9837a3ab2b *R/Topology.R
80028ee422a593ed3ee83da40df21397 *R/sysdata.rda
93c1650f2fa5160ca0c001af54e2bb40 *README.md
0a41a581fa58e23d58059448d8d75add *build/vignette.rds
629d8e932faf7a3a8724e2feba28cff2 *data/ExampleDb.rda
4eda2d480c143a6a24a4ac186eda1c86 *data/ExampleTrees.rda
b034dfc6972e3bdd19b8801d55ac4b7e *inst/CITATION
769383a43ff88ff8ba46792363773a8c *inst/doc/AminoAcids-Vignette.R
5ef45c121608330c741efbe06f88024b *inst/doc/AminoAcids-Vignette.Rmd
b1ecaab3aff8b7cb04c9ae5a82a5578d *inst/doc/AminoAcids-Vignette.pdf
4dc4b79b3b7af4d6e6a16aee03144b3d *inst/doc/Diversity-Vignette.R
d6d5f8c14e2d96e62216c656087fd1a3 *inst/doc/Diversity-Vignette.Rmd
cf1b8069f14bb276369c0d118d65c661 *inst/doc/Diversity-Vignette.pdf
c79ee7539b6516f9139d912470059ac9 *inst/doc/Lineage-Vignette.R
64e4930dae78d9b170c53fb27d740ae9 *inst/doc/Lineage-Vignette.Rmd
57c5b6f19a8f4fe8b65c2967389c57af *inst/doc/Lineage-Vignette.pdf
992842730e2fb10e32081c3981f879cf *inst/doc/Topology-Vignette.R
88a8cbbac52bf8d34ecbeb60dd5ba22e *inst/doc/Topology-Vignette.Rmd
0142792fe1cfeeab9e29734451745c54 *inst/doc/Topology-Vignette.pdf
691999509c3788524d06f82b3a82eafd *inst/markr/build.R
a9d1d1d3adacad855a87f97122d7deee *man/ABBREV_AA.Rd
13bf964a5e2d342c91185034bf2bb2cb *man/ChangeoClone-class.Rd
6f55697229268806bef6a10717678c02 *man/DEFAULT_COLORS.Rd
2f5297b800bdc59c56e53cab0dba9f83 *man/DiversityCurve-class.Rd
979279c716f5129eab4081411788e0a6 *man/DiversityTest-class.Rd
8becef64e2eae19d3a23290cd48a193a *man/EdgeTest-class.Rd
7cbe9e01a367a38af1cb8c90f3e74e98 *man/ExampleDb.Rd
f37509d5350c4a6b4b70a27547011fcb *man/ExampleTrees.Rd
10c34071f6e3ba2efde71291511649a7 *man/IMGT_REGIONS.Rd
c3c727588288b411491b2de77713ec4a *man/IUPAC_CODES.Rd
6d59f161167f08049402ac8426c05793 *man/MRCATest-class.Rd
55fa91edb53241cd86b12f9a9fc51362 *man/alakazam.Rd
db19819685d940da24bd3022a9d4e8be *man/aliphatic.Rd
a1831c858f63a42ad221d7d919ac1bef *man/aminoAcidProperties.Rd
62e22a8308df65fd37ec51a25a30f3d3 *man/buildPhylipLineage.Rd
bbfdb6340b92a396e2b4bb5f15cd5633 *man/bulk.Rd
90ded5990cae15e9a663e2390f29c06b *man/calcCoverage.Rd
8323086d27b4649a08b53ab31e443fd5 *man/calcDiversity.Rd
f5d0c57b59e2dc17cc82c1d59e29d4dd *man/charge.Rd
185975302ba9e3880b36671070956111 *man/collapseDuplicates.Rd
4bdd6c4b5cbd60f9d48f5a8100b9109f *man/countClones.Rd
d309801c71d416ec1a1f93acf6ddd31e *man/countGenes.Rd
99fe6c883f633ea33c0406f07b955776 *man/countPatterns.Rd
2a6f39be206b1583a18f5b864d204f0b *man/estimateAbundance.Rd
8547083d24169e3522ef3f7d4b62dc29 *man/extractVRegion.Rd
d9bcf6fa4885d0682e7f951faf7f2254 *man/getAAMatrix.Rd
f3d1c78e3419a6d133ac41d1b340edb6 *man/getDNAMatrix.Rd
b0cca26c9b43a786937622e56253d96f *man/getMRCA.Rd
4bfa64e2fda7f8e763583ac0db37ac53 *man/getPathLengths.Rd
605720493f605a1e44ace2cce07822f3 *man/getSegment.Rd
32bb08194217d09ee7ed3a3baf8667e2 *man/gravy.Rd
43a957cfa4f3285543fad47363376786 *man/gridPlot.Rd
56bbb424640d95b6e9fcb109c76df6f5 *man/isValidAASeq.Rd
908fbbee2259e9c1dcc3ad26c7f7f4a0 *man/makeChangeoClone.Rd
16c622dc1a843365e20d348978727214 *man/makeTempDir.Rd
2a02699657b4a7fc6c4828128c3d6cb8 *man/maskSeqEnds.Rd
edcf27b9cc3123271f7073703b5592ff *man/maskSeqGaps.Rd
cb1a3c40b114bb4e2503987ec920dd78 *man/pairwiseDist.Rd
a93f7fde10257f4d80ca1a3db58ebcaf *man/pairwiseEqual.Rd
89becaa4bdf1019397e451d162962d3b *man/permuteLabels.Rd
4570dcccbbaadd05459b3cf2dd4473b8 *man/plotAbundance.Rd
13d77615b0b60439cb4839b1144f36e0 *man/plotDiversityCurve.Rd
a6f9379eee8e3d49d7ed6f0b950fe5cf *man/plotEdgeTest.Rd
6ab45372b605cabb0fb80b3d2a7b4cc6 *man/plotMRCATest.Rd
de66765fa28fad7aa3de2fc5ec85c6f7 *man/plotSubtrees.Rd
57f38289101ef92fa9db938e09766869 *man/polar.Rd
539999ca21d655d5e7bb96f0c0f128c7 *man/rarefyDiversity.Rd
749b4b8b9daca586ea634d209ecbaf74 *man/readChangeoDb.Rd
7cc1917257918b65d8ff2c5e0f47e93c *man/seqDist.Rd
f5e27a7fa978350281f109893235c4d4 *man/seqEqual.Rd
1e0a5d095b881bde9dfa4603903b23e5 *man/sortGenes.Rd
4551455c0ab7d85eba44ccab82ddccd5 *man/stoufferMeta.Rd
636a225c9c90626bdeda60cb8c3f4d11 *man/summarizeSubtrees.Rd
6b7a7875c6dbd679c0c8bcb671581755 *man/tableEdges.Rd
059da9cc0d23f753fbacd8d65488d799 *man/testDiversity.Rd
6afa9381da1049bfa5784d60a623b60b *man/testEdges.Rd
042d002aab3b14029a92891b9c4ce161 *man/testMRCA.Rd
4e82d224ec3508acc060e174c9e132a8 *man/translateDNA.Rd
8242a3df101301f23473a572115fc432 *man/translateStrings.Rd
0fae9e0a11ec04f6fc43723538408b95 *man/writeChangeoDb.Rd
3474513d1d71790e2f5d773d9d22eda7 *src/Init.c
f95ea0148d6d5b0259273b400b3f23b2 *src/RcppDistance.cpp
a6bad6d6c6516427ac7967e7d4594746 *src/RcppExports.cpp
5ef45c121608330c741efbe06f88024b *vignettes/AminoAcids-Vignette.Rmd
d6d5f8c14e2d96e62216c656087fd1a3 *vignettes/Diversity-Vignette.Rmd
64e4930dae78d9b170c53fb27d740ae9 *vignettes/Lineage-Vignette.Rmd
88a8cbbac52bf8d34ecbeb60dd5ba22e *vignettes/Topology-Vignette.Rmd
