b994c0146e82788f92bb95ef60f86a2e *DESCRIPTION
6251613cec5dcb32ce5ceb84050a53ae *NAMESPACE
180b2adae90d9e263e5774f8a96bda4e *NEWS.md
4f575a839d871b3e35beb7ed1283d768 *R/Alakazam.R
9bacdbf9fdf6b34d796247445fa65050 *R/AminoAcids.R
e05a50654991d8d4f3cae1e7756c4e9e *R/Classes.R
40fd403cbcced89aea2751506861845f *R/Core.R
f4a71b840d1896ce67d2db391e462fe1 *R/Data.R
f19226bba3940267805ebd3e78802a26 *R/Diversity.R
84fa4fe23d8c5e29ed1b31540b0839ab *R/Gene.R
b0fdcdba439868639deede6698a7c404 *R/Lineage.R
08ff9f5f5f7f9e32764174d565cc86d9 *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
392b6fc40f91ceb1d0c59eff60e71169 *inst/doc/AminoAcids-Vignette.pdf
4dc4b79b3b7af4d6e6a16aee03144b3d *inst/doc/Diversity-Vignette.R
d6d5f8c14e2d96e62216c656087fd1a3 *inst/doc/Diversity-Vignette.Rmd
64f27508e8a6cc8bbc72d225f985c0c3 *inst/doc/Diversity-Vignette.pdf
c79ee7539b6516f9139d912470059ac9 *inst/doc/Lineage-Vignette.R
64e4930dae78d9b170c53fb27d740ae9 *inst/doc/Lineage-Vignette.Rmd
ee2c6400a7215249f85498ae940ae767 *inst/doc/Lineage-Vignette.pdf
992842730e2fb10e32081c3981f879cf *inst/doc/Topology-Vignette.R
88a8cbbac52bf8d34ecbeb60dd5ba22e *inst/doc/Topology-Vignette.Rmd
a7a8e71080cf767858728f9df1acff9c *inst/doc/Topology-Vignette.pdf
691999509c3788524d06f82b3a82eafd *inst/markr/build.R
3fa8036ba322c0c9a30473bba1f94c32 *man/ABBREV_AA.Rd
57267a638ffd78c3116c4304300f1200 *man/ChangeoClone-class.Rd
ff165af28de97c724e5d63d77f10d004 *man/DEFAULT_COLORS.Rd
71778f8482a4abef27ab8efb50c79541 *man/DiversityCurve-class.Rd
066fb2840fb784dcb80e1065faa4bd18 *man/DiversityTest-class.Rd
12acd15af1c371443e24381a1aa78923 *man/EdgeTest-class.Rd
e471695a5203e882c7fa7265ac00193f *man/ExampleDb.Rd
0e7a4cb5e616480f71662c74fc0d4b7c *man/ExampleTrees.Rd
0a2ec0ab08de15ef3de6bcca53450233 *man/IMGT_REGIONS.Rd
f35e04678852edea918650f674a85990 *man/IUPAC_CODES.Rd
a01dd8315c0d5c27951591a4e2b5bee8 *man/MRCATest-class.Rd
5c53113f08c3908758d10b89e3e50d99 *man/alakazam.Rd
f626ba1590d65104acc24ca233aa1849 *man/aliphatic.Rd
bfda30c20c44d896f44cfd84138bbf9d *man/aminoAcidProperties.Rd
229886c9099e849018cffb86675e157a *man/buildPhylipLineage.Rd
7b1c2d8c326b8b88cf0daf21360cfc4a *man/bulk.Rd
e918c660515307baa239a7bf1f95dcd7 *man/calcCoverage.Rd
c909e75560e1dd9ce33123a2df3de342 *man/calcDiversity.Rd
85b3bc1949a5ffb6cd1a806ad59bed34 *man/charge.Rd
d1cb6f6252160ba8b8938dd7e7c0a1b3 *man/collapseDuplicates.Rd
d38d255337381fa1c2bdd50991a1b153 *man/countClones.Rd
413261791b62e4fe9c30946a6a2eb776 *man/countGenes.Rd
fa1b66aa4339599f0cf4136a5f623713 *man/countPatterns.Rd
b10b0ca86dc3463596896ac707f7769d *man/estimateAbundance.Rd
7696f27f58b9f5c5a2dfddc2ec8509e4 *man/extractVRegion.Rd
7b5a7e031d4f0c0d13594de33ee0f709 *man/getAAMatrix.Rd
1e8dc92dfc37be43bcacf06d1ca3d830 *man/getDNAMatrix.Rd
78d64082e0b13571667390554a6d14ca *man/getMRCA.Rd
0e2039e08f6f02735bc17b135e86cff8 *man/getPathLengths.Rd
4e52a2a286385664a789d1d8e3c20610 *man/getSegment.Rd
8d99232e73fb1dd95c1af4ff00dba6c5 *man/gravy.Rd
cbfc11c787fcd0af82e6d85251c814f8 *man/gridPlot.Rd
3df00707daa46509e850913867515707 *man/isValidAASeq.Rd
c988de11cc6bc46c3c18bac6b17a3e19 *man/makeChangeoClone.Rd
f4f598c150b698ba7e320b62f2cfb4a7 *man/makeTempDir.Rd
d47f697ec7a5804df84effbbbc1198bf *man/maskSeqEnds.Rd
0a33224745a12dd3728bc29c8a78f3e7 *man/maskSeqGaps.Rd
c370cb752709435b56dc4aa8bc8adbe4 *man/pairwiseDist.Rd
6f648fbaccfe44a156aaa87b4d76f93c *man/pairwiseEqual.Rd
f46421532ca914db5d10fd9b68346eac *man/permuteLabels.Rd
edf95b94953348bcfcd6314ad26bda53 *man/plotAbundance.Rd
ef81058ff93164eec1e76bdad7fc9324 *man/plotDiversityCurve.Rd
32e6b27d53c81d08813e5100c2662361 *man/plotEdgeTest.Rd
5fb43614531e64999465e3ed88dff0b3 *man/plotMRCATest.Rd
ae078bea7ecc6aee73f2c6f665757486 *man/plotSubtrees.Rd
b0a9d99f81b60b95090f2426982b1c4f *man/polar.Rd
1fc976f8431b911636239431f079d05d *man/rarefyDiversity.Rd
9a8cb070220083bc6df2e24553ae047a *man/readChangeoDb.Rd
a10ddbcc54588c8d70a69824f1a56710 *man/seqDist.Rd
780126e216a3589ad3aaade26cb47712 *man/seqEqual.Rd
93ac392f02b67fb75f784b98dda42dda *man/sortGenes.Rd
412197474d2456ffb5b31e2bfda98865 *man/stoufferMeta.Rd
69a93101789850451b5338bcc22647ee *man/summarizeSubtrees.Rd
38ccd05c06ae506d4f682c7f6c350b4a *man/tableEdges.Rd
ab0bc97423f3d80ef06847b1bf48c368 *man/testDiversity.Rd
139ea8242082be829035b9b7809f272d *man/testEdges.Rd
49c7c8a80c52fa511ed82efdec5dcd74 *man/testMRCA.Rd
a136d4059c0658076a0f6ede79bf84bc *man/translateDNA.Rd
11d289468204e171a0367af3a1f68c60 *man/translateStrings.Rd
bc2b9155d14f688ffe19db49ffb06af7 *man/writeChangeoDb.Rd
f95ea0148d6d5b0259273b400b3f23b2 *src/RcppDistance.cpp
c7962bdb99ca3b96984bef924a59ad9e *src/RcppExports.cpp
5ef45c121608330c741efbe06f88024b *vignettes/AminoAcids-Vignette.Rmd
d6d5f8c14e2d96e62216c656087fd1a3 *vignettes/Diversity-Vignette.Rmd
64e4930dae78d9b170c53fb27d740ae9 *vignettes/Lineage-Vignette.Rmd
88a8cbbac52bf8d34ecbeb60dd5ba22e *vignettes/Topology-Vignette.Rmd
