b0c25b9f9903919c6bf628a3b561c17e *DESCRIPTION
adf18d10ac40be8cf1437a87ccb67dce *NAMESPACE
7a4588642124f89d2bdd72ca8a1041ed *NEWS.md
61680611889e9621a51738f31e454425 *R/Alakazam.R
be946ccc7f91378c5a61bf426d1eacd2 *R/AminoAcids.R
f6e0d1fce17fe087df552218004a6be9 *R/Classes.R
6425a23855eeea913faa8855a5ebbcc0 *R/Core.R
51bfc71c507d073cb7433664f14beef7 *R/Data.R
86e564b8b709c13ca72e80296a455980 *R/Deprecated.R
a9757b17fd8ac61aebd8965d579dd382 *R/Diversity.R
1e9d126dc379482d08a77c0f6fb75cd6 *R/Gene.R
4415de7ad84d739c5547ca269404771a *R/Lineage.R
6f8a72642969fd382cd8f88bc18e6b24 *R/RcppExports.R
c890aa0120f50696930a26692efa56be *R/Sequence.R
0727444d4b16f44f29bb4461adfa4e50 *R/Topology.R
def92a4fe63ca7bcdba22c3a382dbced *R/sysdata.rda
168be8c19aea742d3b03dfa02f144296 *README.md
95195322faec7d9fa966df1a18fdfeb2 *build/vignette.rds
5f9bc5c5ec7049903abee0ac3546c811 *data/ExampleDb.rda
f9dc276a0e661219b4340560d30c63a1 *data/ExampleDbChangeo.rda
40e39c63a2fe73a4b9013d06c55468e9 *data/ExampleTrees.rda
b034dfc6972e3bdd19b8801d55ac4b7e *inst/CITATION
a95ec89508681a6627901170cc7e4628 *inst/doc/AminoAcids-Vignette.R
fb827b4caa7ec3d7a244801343f81e1f *inst/doc/AminoAcids-Vignette.Rmd
309be4995cdb052e3c18bd50a568d112 *inst/doc/AminoAcids-Vignette.pdf
700fa8bdfc792634f2b5873186104d0f *inst/doc/Diversity-Vignette.R
4f592e6548cf200ba8427a0e0197ade9 *inst/doc/Diversity-Vignette.Rmd
72ac0f47ac9cec1b296561ebbe7dde67 *inst/doc/Diversity-Vignette.pdf
316b9e92df2066a0f3f72ec7d8bb1022 *inst/doc/GeneUsage-Vignette.R
27d4803bb5f0337eb9b45fbbecd0cf33 *inst/doc/GeneUsage-Vignette.Rmd
ddf601b2bbd916f9696d946d7a8a6514 *inst/doc/GeneUsage-Vignette.pdf
9a06e7ab9acf7316d267a736ea0624f1 *inst/doc/Lineage-Vignette.R
5491dc02241a9cafe01569a78bb524ff *inst/doc/Lineage-Vignette.Rmd
e82f55f6fee8f7348e6f0af611eb639f *inst/doc/Lineage-Vignette.pdf
e20fababa3ab7cde6ffcc92b8b2b3ee5 *inst/doc/Topology-Vignette.R
8f9409c731317d6dadeb9f7733b85dad *inst/doc/Topology-Vignette.Rmd
2f16bfaad8550c6d96dc0e5fa87435c0 *inst/doc/Topology-Vignette.pdf
987475fe1f56c385e720c6afd798dd08 *man/ABBREV_AA.Rd
12bc2f6e5c83021ba446013f93f2c819 *man/AbundanceCurve-class.Rd
13bf964a5e2d342c91185034bf2bb2cb *man/ChangeoClone-class.Rd
a84a6d4edd8410275bb1abd5a463ad32 *man/DEFAULT_COLORS.Rd
e8cf58a2dee521487a4c4c64af7a793f *man/DiversityCurve-class.Rd
ddc49fed05c59121028f0dabecbe5fb1 *man/EdgeTest-class.Rd
407424a705d79f858d4e57db2caab842 *man/ExampleDb.Rd
40db6c9c2338f5fee3bc9d1c8c9ce4e9 *man/ExampleDbChangeo.Rd
6e69b6b8867ec8ce3d7a0df5da568603 *man/ExampleTrees.Rd
8715b738946f7c22ce18b077e0f8b724 *man/IMGT_REGIONS.Rd
68c7b9b6f970ddf83b5367a7aac77f54 *man/IUPAC_CODES.Rd
4d8441622f8bbb14de45524ceecbe737 *man/MRCATest-class.Rd
2ff2d4ad04c36645af1cb93497b1df21 *man/alakazam.Rd
db19819685d940da24bd3022a9d4e8be *man/aliphatic.Rd
423abfd260abd878bebd72bbaf3799fe *man/alphaDiversity.Rd
acee9fd93bc965e961a1d2051e1d036e *man/aminoAcidProperties.Rd
a8d03c199086e18e26fd673624ffa1a4 *man/baseTheme.Rd
193b5718b7d6104f6cd63d453d2cdc9d *man/buildPhylipLineage.Rd
bbfdb6340b92a396e2b4bb5f15cd5633 *man/bulk.Rd
c686bdeedc7abc3277241668dfe4bb2f *man/calcCoverage.Rd
af307d6e0209dbd3acaf15c8ec4c8295 *man/calcDiversity.Rd
f5d0c57b59e2dc17cc82c1d59e29d4dd *man/charge.Rd
995aabe2f257ba72862d5b226ce03c66 *man/checkColumns.Rd
7c682c648b3a05217b526850f09d1b42 *man/collapseDuplicates.Rd
c3719294a76cb1dc606b0115b935be90 *man/combineIgphyml.Rd
553a942a2edc4f4bce8ad4908925ef20 *man/countClones.Rd
7baf7d00b099d04c8cb164082a8fe468 *man/countGenes.Rd
1a24fe55cec62c30e5119214c5497641 *man/countPatterns.Rd
228c0d1d4a6fc2744f10623b6342ead8 *man/cpuCount.Rd
2a319c89da2b5e3d33054136acfa3d91 *man/estimateAbundance.Rd
9dd006c3a64d4b51deafeecdbb805fac *man/extractVRegion.Rd
d9bcf6fa4885d0682e7f951faf7f2254 *man/getAAMatrix.Rd
f3d1c78e3419a6d133ac41d1b340edb6 *man/getDNAMatrix.Rd
da9177951218d3a90104d18255531f86 *man/getMRCA.Rd
d97054f355e98a82cf5a5a806526ed5b *man/getPathLengths.Rd
9e3ab8d4148c1100575f13e8b8c6fad8 *man/getSegment.Rd
76697bcf036a02fbe6ddb7f351926ca9 *man/graphToPhylo.Rd
ebd8bf4d329181cffdec5346ad8721ee *man/gravy.Rd
43a957cfa4f3285543fad47363376786 *man/gridPlot.Rd
712ba0d0a84b8c88eabae20a5f4a298b *man/groupGenes.Rd
56bbb424640d95b6e9fcb109c76df6f5 *man/isValidAASeq.Rd
06c223e80ce92f32f5a2c495b9d8a6e3 *man/makeChangeoClone.Rd
16c622dc1a843365e20d348978727214 *man/makeTempDir.Rd
1eeab523917cc47d245c324644f4a387 *man/maskSeqEnds.Rd
18ef28997eb2cb4a67ae7f06c4856f6d *man/maskSeqGaps.Rd
c4ee04b0eacd1e93066cc87c0520800d *man/nonsquareDist.Rd
d4afa5c07e9908b4968e5a8d56053ff9 *man/padSeqEnds.Rd
1e23c90638621a4425fc49ced382dc0c *man/pairwiseDist.Rd
a93f7fde10257f4d80ca1a3db58ebcaf *man/pairwiseEqual.Rd
f0e407fd33a9a29bf63240fefb36c724 *man/permuteLabels.Rd
9992507f0b39b569c4eaac2c35e41ebc *man/phyloToGraph.Rd
1464ab02cdbdde56bf43bf2fb09896c0 *man/plotAbundanceCurve.Rd
3a398759982862f3c309f41f5d93f204 *man/plotDiversityCurve.Rd
5b9a7c245bdc2ce91dad0b34777140c1 *man/plotDiversityTest.Rd
b04ce7ad42cc547cad4f6d868ff121b8 *man/plotEdgeTest.Rd
a5b7b7857f7d7af28283f046db9d47ce *man/plotMRCATest.Rd
a2f316fb3a25fb9d7264a991800d13d8 *man/plotSubtrees.Rd
57f38289101ef92fa9db938e09766869 *man/polar.Rd
7c2c3846d5f429596501499da0c9aec9 *man/progressBar.Rd
6649627271c10d1be5d87687c649e762 *man/rarefyDiversity.Rd
749b4b8b9daca586ea634d209ecbaf74 *man/readChangeoDb.Rd
3c998734ff5653afd81c236ebff86ffd *man/readIgphyml.Rd
7cc1917257918b65d8ff2c5e0f47e93c *man/seqDist.Rd
f5e27a7fa978350281f109893235c4d4 *man/seqEqual.Rd
1e0a5d095b881bde9dfa4603903b23e5 *man/sortGenes.Rd
4551455c0ab7d85eba44ccab82ddccd5 *man/stoufferMeta.Rd
a70b6eafc7cbb3753f60afe631379f3e *man/summarizeSubtrees.Rd
68a832553b26782673d82eeaedea750c *man/tableEdges.Rd
3308f5dd254a011be415178f8b17b710 *man/testDiversity.Rd
30c9e033d03b8ae1362aa6bb31de7aa7 *man/testEdges.Rd
20882770192a22a72305d094fbd60a70 *man/testMRCA.Rd
ed2b5d2d9fd87a693a560dd5fd7fdf7f *man/translateDNA.Rd
8242a3df101301f23473a572115fc432 *man/translateStrings.Rd
0fae9e0a11ec04f6fc43723538408b95 *man/writeChangeoDb.Rd
3b377cf40c356ccde3fa098907bfd279 *src/RcppDistance.cpp
abf7eb815358ba8bbf07451999ce055e *src/RcppExports.cpp
fb827b4caa7ec3d7a244801343f81e1f *vignettes/AminoAcids-Vignette.Rmd
4f592e6548cf200ba8427a0e0197ade9 *vignettes/Diversity-Vignette.Rmd
27d4803bb5f0337eb9b45fbbecd0cf33 *vignettes/GeneUsage-Vignette.Rmd
5491dc02241a9cafe01569a78bb524ff *vignettes/Lineage-Vignette.Rmd
8f9409c731317d6dadeb9f7733b85dad *vignettes/Topology-Vignette.Rmd
