c3921640948a96bf267ac5905876335f *DESCRIPTION
ed903e2417a87454d1687b4548db5cd0 *NAMESPACE
3b83f5b47f5fa427a562acc70c3971af *NEWS.md
95b408bd4abf6759c3e9b5a7fca7ec06 *R/Alakazam.R
9bacdbf9fdf6b34d796247445fa65050 *R/AminoAcids.R
598c705060d7493b8c917d0b7855cfe8 *R/Classes.R
0b817e2919a322efeb448aaebe8ff002 *R/Core.R
f4a71b840d1896ce67d2db391e462fe1 *R/Data.R
91f9e3143db9c3fa86c8080e3a5c5d51 *R/Diversity.R
741c2dc2d4c2f99285c89a502feb5145 *R/Gene.R
0f259009768ea87f09ea6faadd450288 *R/Lineage.R
16a1834b1f32d01fa94e3e6408361cb8 *R/RcppExports.R
61079bea8440fd57a2890e0ee5672c6f *R/Sequence.R
045bfe13efc6319d066d064975018722 *R/Topology.R
2be0a5362455c544103dcae08438ad32 *R/sysdata.rda
2615b26313f998cf9856f149f418f5d4 *README.md
987086a17a0c68f4c8ca778630c4b896 *build/vignette.rds
3d37dbf47ab43f43b0333666b76a0698 *data/ExampleDb.rda
4eda2d480c143a6a24a4ac186eda1c86 *data/ExampleTrees.rda
b034dfc6972e3bdd19b8801d55ac4b7e *inst/CITATION
769383a43ff88ff8ba46792363773a8c *inst/doc/AminoAcids-Vignette.R
5ef45c121608330c741efbe06f88024b *inst/doc/AminoAcids-Vignette.Rmd
7359b6c14eebc271dd21c9c28998f419 *inst/doc/AminoAcids-Vignette.pdf
3383a8da6dde698a98711a902d62a7d7 *inst/doc/Diversity-Vignette.R
f1e1ac4eba39d19541c545330ead34b4 *inst/doc/Diversity-Vignette.Rmd
17e4e7230ddde1d2f9ca3a1620cdeac0 *inst/doc/Diversity-Vignette.pdf
ddc3b83b2023540dd65b3cecacd3d7d9 *inst/doc/GeneUsage-Vignette.R
3640f68c150cfa03dab6d21dea08a2f1 *inst/doc/GeneUsage-Vignette.Rmd
606a617e6b31377208413d69012628de *inst/doc/GeneUsage-Vignette.pdf
c79ee7539b6516f9139d912470059ac9 *inst/doc/Lineage-Vignette.R
5797bd84f5db571df93216677f4d5ff3 *inst/doc/Lineage-Vignette.Rmd
e1f643a608377b98737f4e0ec5ad6df0 *inst/doc/Lineage-Vignette.pdf
992842730e2fb10e32081c3981f879cf *inst/doc/Topology-Vignette.R
bf365971a4fd926b5ad1f3da4e19514a *inst/doc/Topology-Vignette.Rmd
dea1785fb53e84041ae4cac82455e6b1 *inst/doc/Topology-Vignette.pdf
691999509c3788524d06f82b3a82eafd *inst/markr/build.R
a9d1d1d3adacad855a87f97122d7deee *man/ABBREV_AA.Rd
fedc27eff79bebb6b814c2d04af87bc5 *man/AbundanceCurve-class.Rd
13bf964a5e2d342c91185034bf2bb2cb *man/ChangeoClone-class.Rd
6f55697229268806bef6a10717678c02 *man/DEFAULT_COLORS.Rd
65da45ea5c7cca11a660e4eb44ea21a9 *man/DiversityCurve-class.Rd
c519494600aead3a0f5bd9087182a5cf *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
30bc8d15143218431ce2afa53fa7049e *man/alakazam.Rd
db19819685d940da24bd3022a9d4e8be *man/aliphatic.Rd
a1831c858f63a42ad221d7d919ac1bef *man/aminoAcidProperties.Rd
2c1c0ac19587818a201e7d945f941ec0 *man/buildPhylipLineage.Rd
bbfdb6340b92a396e2b4bb5f15cd5633 *man/bulk.Rd
90ded5990cae15e9a663e2390f29c06b *man/calcCoverage.Rd
8323086d27b4649a08b53ab31e443fd5 *man/calcDiversity.Rd
f5d0c57b59e2dc17cc82c1d59e29d4dd *man/charge.Rd
0a92493d7bcbd1058510be35635a17b8 *man/collapseDuplicates.Rd
4bdd6c4b5cbd60f9d48f5a8100b9109f *man/countClones.Rd
a2f4b3c8fabee38120403337344c67e4 *man/countGenes.Rd
99fe6c883f633ea33c0406f07b955776 *man/countPatterns.Rd
15527489681ac6735ec2ea0f129c01e3 *man/estimateAbundance.Rd
325ec5e08c9c4a68ca02c3289038322f *man/extractVRegion.Rd
d9bcf6fa4885d0682e7f951faf7f2254 *man/getAAMatrix.Rd
f3d1c78e3419a6d133ac41d1b340edb6 *man/getDNAMatrix.Rd
b0cca26c9b43a786937622e56253d96f *man/getMRCA.Rd
4bfa64e2fda7f8e763583ac0db37ac53 *man/getPathLengths.Rd
50b00879364a1a20c951fb5f6187f7cc *man/getSegment.Rd
32bb08194217d09ee7ed3a3baf8667e2 *man/gravy.Rd
43a957cfa4f3285543fad47363376786 *man/gridPlot.Rd
56bbb424640d95b6e9fcb109c76df6f5 *man/isValidAASeq.Rd
b9a9a3ceb051dd1b075068c22643ccf0 *man/makeChangeoClone.Rd
16c622dc1a843365e20d348978727214 *man/makeTempDir.Rd
1eeab523917cc47d245c324644f4a387 *man/maskSeqEnds.Rd
18ef28997eb2cb4a67ae7f06c4856f6d *man/maskSeqGaps.Rd
d4afa5c07e9908b4968e5a8d56053ff9 *man/padSeqEnds.Rd
1e23c90638621a4425fc49ced382dc0c *man/pairwiseDist.Rd
a93f7fde10257f4d80ca1a3db58ebcaf *man/pairwiseEqual.Rd
89becaa4bdf1019397e451d162962d3b *man/permuteLabels.Rd
4f76c236f6dd8e0c52eb435d5c81c669 *man/plotAbundanceCurve.Rd
18ba54f9f17ffaf1c90a435f903f5d40 *man/plotDiversityCurve.Rd
cb43639baed1ac38886d996c113ea536 *man/plotDiversityTest.Rd
a6f9379eee8e3d49d7ed6f0b950fe5cf *man/plotEdgeTest.Rd
6ab45372b605cabb0fb80b3d2a7b4cc6 *man/plotMRCATest.Rd
de66765fa28fad7aa3de2fc5ec85c6f7 *man/plotSubtrees.Rd
57f38289101ef92fa9db938e09766869 *man/polar.Rd
762e65cb16d72123a1c55b8180a0eb9c *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
7785154c537e8a938e81bb569fdd0eac *src/RcppDistance.cpp
98d04f37a70d0d187d43537312ef329a *src/RcppExports.cpp
5ef45c121608330c741efbe06f88024b *vignettes/AminoAcids-Vignette.Rmd
f1e1ac4eba39d19541c545330ead34b4 *vignettes/Diversity-Vignette.Rmd
3640f68c150cfa03dab6d21dea08a2f1 *vignettes/GeneUsage-Vignette.Rmd
5797bd84f5db571df93216677f4d5ff3 *vignettes/Lineage-Vignette.Rmd
bf365971a4fd926b5ad1f3da4e19514a *vignettes/Topology-Vignette.Rmd
