42ad0e6eaf36e1792dd186582a7efbde *DESCRIPTION
190f395e8ef5f54a96bf6b9b11ae922d *LICENSE
9abc7a3cdc4ec0eff37565aa8734bf85 *NAMESPACE
5404764cf976258201e492598dd0e2f8 *NEWS
4fbad19753016493c8c3a160434702ce *R/RcppExports.R
8cff7c905fb82ef6fa5439e90edeed09 *R/SNPsites.R
066fd25918fbf5f2c2d8b7268d19e8d0 *R/addMSA.R
d97eb114023a87d74e67a87fb9f3ec7e *R/allSitesName.R
31b67599c3188130c69857e8a6d57c35 *R/as.data.frame.R
3c9b28d3a05927baa4bfd2e9364ea2be *R/extractSite.R
b296113a783b672443455426a28ee702 *R/extractTips.R
7ff83ba4331e31746f51bd59b5ed578c *R/fixationIndels.R
0c41295178e8df693f8af16484ae4d8a *R/fixationPath.R
f9fc3b7059f95a70f0c45cc0f67edb35 *R/fixationSites.R
7e526f8478d974d2e4d95ceededdd5d6 *R/groupTips.R
b21072a18e68dd7aaea0f82656537497 *R/lineagePath.R
70bffbae2e0603a99bcf099f5b8d2649 *R/paraFixSites.R
d628500f8fdc5a9beaf8146c63a38738 *R/parallelSites.R
fe7bb6788401d118175a04ecaa7c5d71 *R/plotFixationSites.R
16f7725324db8469d48e2398f169b167 *R/plotFunctions.R
d39ec821424448a4d1976311a48c25d0 *R/plotMutSites.R
140b3418d55d0af8985caa2571aa80b6 *R/plotParallelSites.R
2f0de60659ed2f12ed40d51c3d9fee29 *R/plotSingleSite.R
8473478d73b3feb5bd0de68dd0a12467 *R/printFunctions.R
f56d5a1855bc0502d897d5dd02c84162 *R/reexports.R
2bea2f9359b87ccfdeeea42c4e81b239 *R/siteNumbering.R
03487190dea9130bdc651f018faa61aa *R/sitePath-deprecated.R
27b17cb90a63839b920efd6f862e964b *R/sitesMinEntropy.R
0139b1065bfe0edc73aa9c731f31d2de *R/staticData.R
e40edd4b22d890713ba129b582409262 *README.md
0c3af88d377415e536c66a9a379c59bc *build/vignette.rds
ba7f399fae619a8b336db025f36062a3 *data/h3n2_align.rda
cb7a7cc8226cfc18d23c4c9d8e05056f *data/h3n2_align_reduced.rda
a7d18430fd570986f384e5d6ccbd83a9 *data/h3n2_tree.rda
11b4e337247df31471bb285a599ffdc7 *data/h3n2_tree_reduced.rda
ce8b1ca74f5b74d46d683bf618530561 *data/sars2_align.rda
aacef343952c06ada6b472ffb2553bc8 *data/sars2_tree.rda
8e542035dccd677ca8869a8ce6072612 *data/zikv_align.rda
652c908712f4fedb3a76dabb4b04cfc0 *data/zikv_align_reduced.rda
8f7c91558b2418a9b693bc4e4db6deca *data/zikv_tree.rda
68869f42c23d6d1d23edec025f68c8f8 *data/zikv_tree_reduced.rda
4a7af84d2abdc4a34505ebd7f20a5b17 *inst/doc/sitePath.R
ef091bacc2036e02e40fa96c0f46c735 *inst/doc/sitePath.Rmd
2b6472e1a1cb2db84856ec075d9466ac *inst/doc/sitePath.html
0d0930ad876a6c2dfbe4ffec812e7699 *inst/extdata/WNV.newick
ec304b6904d608b49b8c47c747c8672e *inst/extdata/ZIKV.fasta
4253e27f1ef23663eb4939e8c0b03fab *inst/extdata/ZIKV.newick
889a6aa50e6622d6703a0413379b017b *man/SNPsites.Rd
65d3b618e2254c97c3c17a764ed841d7 *man/addMSA.Rd
ee38a7e810cbe109464e51fe8cb8ed26 *man/allSitesName.Rd
ccf48e702148bd04fcb964626bee9b63 *man/as.data.frame.Rd
42d948e5b077e23ddd0f3b4c961f50a6 *man/extractSite.Rd
0e3cbcc7d2de99eede75e903bb42dffa *man/extractTips.Rd
05fd1ba5854e99e6ff377ebc9f8c533d *man/figures/example-1.png
546c22249a708a6cca33f21d45f04810 *man/figures/example-2.png
8e549ef79307ead6c166df7c69dbfc10 *man/figures/plot_fixSites-1.png
7c7eea05ca70311f272c5bf811fb0061 *man/figures/plot_fixSites-2.png
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9ed3e6685da169091fce89c21076f3fc *man/figures/unnamed-chunk-1-2.png
c0642bd689909226035c25254bc54c66 *man/fixationIndels.Rd
33194c7ffa84deeabcc803829186db86 *man/fixationPath.Rd
09fe35294fa64a1d52930e2e71e73f8c *man/fixationSites.Rd
96b076544739ea22bb3c6f8361419e66 *man/groupTips.Rd
876f4f936a1ac14cf5e6e2c1093388dd *man/h3n2_align.Rd
db4d450e0aaea3e4ef1f197c729ebd45 *man/h3n2_tree.Rd
6fcb538127cdc32bc6b3d124794ad825 *man/lineagePath.Rd
11fca1086fcbc4c3f53d78104ae64103 *man/paraFixSites.Rd
13b423f4d80842a60f5ed7ffa37a32d9 *man/parallelSites.Rd
6cd65699d0bad598e042a06d5ec59d4b *man/plotFixationSites.Rd
22bece21fd59dfe625a26fb75676a8e1 *man/plotFunctions.Rd
5d716c32e53777beb329ab42a7ff0ff0 *man/plotMutSites.Rd
d0bf5dc7cce9289100b8bedd7fc1e6fd *man/plotParallelSites.Rd
e41b31782ccde3cc9242a58a12272b78 *man/plotSingleSite.Rd
22ebb49869530d24120e15462816f6f8 *man/reexports.Rd
df2f54034a09c0c19be43e27357a3ae9 *man/sars2_align.Rd
915daab813323cf3513472c5f03510e3 *man/sars2_tree.Rd
11004969b517d6452773f0becf533ce2 *man/setSiteNumbering.Rd
84e749fbe3c39466db75b6968fa4e33a *man/similarityMatrix.Rd
a03381f1914b128d67e471fbd97b7760 *man/sitePath-deprecated.Rd
c9377a8a37212d7135d71e31c5aff2d1 *man/sitesMinEntropy.Rd
c2183ca56455a72b00c381e3f1e576e9 *man/zikv_align.Rd
da0bf22610098ead73f02e7412f5808f *man/zikv_tree.Rd
82eea57b139ac21986ce760e754e423f *src/RcppExports.cpp
f650010269551e3f6dee70e39ec5bbb1 *src/lumpyCluster.cpp
face396efedd174b5da0a12d4799d51a *src/lumpyCluster.h
1ed0b23cc648569a11bf6b58ce7f9bf5 *src/minEntropy.cpp
687c1a06977b0e926298c280a45f5b3e *src/minEntropy.h
9cfe19f3b41dc3dc2e81c0646474dacd *src/searchNode.cpp
b43be98f41e312bf42194f9f7f837cd1 *src/searchTree.cpp
2df841f0c61c5a0d6fbd89d869fe33c0 *src/treemer.cpp
09107c7bd228ef4b6be5dc8abddf7226 *src/treemer.h
a3acae1c220d7318ec426420e9426edc *src/util.cpp
17a9f36bddfcb9184cddd58be4dfdec5 *tests/testthat.R
f02c701cac44153969629f23edbdccb6 *tests/testthat/test-SNPsites.R
9e9fde3235df578f3fd9b0e2b87b1767 *tests/testthat/test-addMSA.R
e942e987ae8259e2e8e28a6d2547c30b *tests/testthat/test-allSitesName.R
38a23e2f77ca9b25cfc0cd637c7ebd42 *tests/testthat/test-as.data.frame.R
3be580864b13670540a4ded86a0d5106 *tests/testthat/test-fixationPath.R
d4f88d0e15c52ddf7cdba94545920844 *tests/testthat/test-fixationSites.R
827bed24e5c842e59851fabe5cc2f8d4 *tests/testthat/test-groupTips.R
cbb6cbab341456a36711fd7fdd39d9f3 *tests/testthat/test-lineagePath.R
d09e890dfbc9606f28347acf062b0172 *tests/testthat/test-multiprocessing.R
ebd1945f839d05ecd95d9d2432f03dc5 *tests/testthat/test-paraFixSites.R
eb3f11bc14789ff8941cd32ac45fd940 *tests/testthat/test-parallelSites.R
5506d802cafad1c7df59cb4c0a0c53f7 *tests/testthat/test-plotFunctions.R
4590aa288b897abf1bdc6b22ec8e32e9 *tests/testthat/test-plotSingleSite.R
1e0799c8222acecacdde03e26351b88f *tests/testthat/test-printFunctions.R
438783482bfa4415353422d74d14befe *tests/testthat/test-reexports.R
9696d753fbd5d8f3f7bc78fa1dab83cb *tests/testthat/test-similarityMatrix.R
9f65e487a05289249a1b9ec1e2bf00bf *tests/testthat/test-siteNumbering.R
8ffd769e68617af9bab3f48446ada5fd *tests/testthat/test-sitesMinEntropy.R
ef091bacc2036e02e40fa96c0f46c735 *vignettes/sitePath.Rmd
