8c25bafc9542a85e85ce520369f4ee91 *DESCRIPTION
0acd583a23392fae76f3eb52c7b1f1bb *NAMESPACE
96a1ec3c41fb90c3faa415af71660658 *NEWS
87e5c967bd0095f61c976d9380f86cb8 *R/Coalescent.R
2452638c6d8b55869e5aa857eb7c4dd0 *R/Densi.R
93a653a2fa4b10e88aab1067528dddac *R/F3X4.R
738b786864e52d06e1c207d84c61cc13 *R/RcppExports.R
7c8048d8d21dd4a427d2a7ee4a1c46d5 *R/SH.R
c03b06289fa093d49bb4b4d871e534e7 *R/SOWH.R
59567454ed1bc26f5dfbe9b370498e62 *R/addConfidences.R
3a3d01773a15843bcc60e936821ff534 *R/ancestral_pml.R
14a7cfab8c2d01b8db94a579d8ebeb9c *R/bab.R
b0eb6d72dbb77d072fb1eec2351371ed *R/baseFreq.R
bd2c859c1f69a94924ee90fa365df647 *R/bipart.R
c37c330d7c092a4e6e466739eb1064b2 *R/bootstrap.R
061c98db08f8be1869c97b081ffecac1 *R/candidate_tree.R
36db49e185c388994cde4a933554d2ca *R/cladePar.R
aa093860dd55cf8464453e408452d0a8 *R/clanistic.R
e8f62008dc9ad8901a16eeaaa4e178e0 *R/codon.R
34251082de150ed5cbc816329d9dd9fc *R/codonTest.R
8d35028ef5cc61b0a73b24cb1a78ea09 *R/delta.score.R
fbcb4925ff4b31f09f7803194fec7a05 *R/discrete.gamma.R
940aa04f153afa4a1a1a39435f6b903a *R/dist.p.R
d27a155722f83ccb35fc8aa904fc3392 *R/distSeq.R
634504669ec6b180f0db2eba6859f7ef *R/distTree.R
788c47f83ab5efb85b18e57349190bca *R/draw_CI.R
c6b96e44d3339d3c6247d966db63a86d *R/fitch64.R
89f8a9268b83288ac06183ad93dc0d1f *R/hadamard.R
461a440c1aa2ade7fe69d685c86c8eb2 *R/hash_phylo.R
bbfbf5af03a47771a78aba47189bbcfa *R/image_phyDat.R
7d5eee6139bb3b1463f024749e01a96a *R/lento.R
a98ef4022b72f150d249c52dc213a971 *R/mast.R
a6c7c69adae722a90d0fb9da5bec92df *R/maxCladeCred.R
2962596c0128ea0296d44a666ca1bb35 *R/modelTest.R
498478344310c2d8595f4a0eb126c075 *R/neighborNet.R
266e2ebeec2b527f0ed1fc4911872559 *R/networx.R
2ebe39a9186cd6e5b85281eeb75cbe47 *R/parsimony.R
a9218b81959033f39515f770145a0dd6 *R/phangorn-package.R
2f8e463a9250e1162f51b06e28df9ab4 *R/phyDat.R
ab91f813696d90f20d118b213fc89564 *R/phyDat2.R
32bba9f64090d53fe942c09b62270e8a *R/phyDat_conversion.R
6dbc91407e6f482de39709b35caf7a89 *R/phylo.R
b032e3212c94ee3cc502b53ee4f0077e *R/pmlMix.R
353983da3a22580082f7dfbac2d97f4c *R/pmlPart.R
08eefc8b3f70e1c127afa95d5e0be591 *R/pmlPen.R
85f157bfa9c0f5a8f21e00f1e6fed477 *R/pml_bb.R
dc9874d40921650d1fc0a50d611bf53b *R/pml_control.R
0024c7b9d1c40c5f5b07a53a3042f176 *R/pml_generics.R
14d1760959bd19a7a26f75785df0df52 *R/read.nexus.splits.R
d889c581f70caf11d7f320da9324027b *R/read.phyDat.R
67f10f68fccf7ac989920c9773f2b48d *R/sankoff.R
0c6b792b0534baed4dba4b7e8f4a18ed *R/simSeq.R
bb2c3d0db36e1cdcc9ba909128c4cf10 *R/splits.R
0ab9e7107f3df4e64a5f56e741aa4ecf *R/splitsNetwork.R
24938bfda29892ebf9aa6384f2ab1248 *R/superTree.R
dcbc5579e8941e63d79f139db0fd0a32 *R/sysdata.rda
167333f92399f3c41877fe2430e7f8af *R/transferBootstrap.R
164e4d5c031f6f03657e0ce161dd465f *R/treeManipulation.R
763fd29a21e8612db2fedfba6a439285 *R/treeRearrangement.R
a93e5aecc49c864ea09737361a1ff8da *R/treedist.R
957a34587abf4d1db45ebdfb8a86dd76 *R/zzz.R
389e1db3da6282ee608b4345f54159ec *README.md
495e52bb75550b9f47c6663a618bea04 *TODO
88b44e14ec365a1e52472378d73223be *build/vignette.rds
4a92b07bcd170e85bd237e460acafa93 *data/Laurasiatherian.RData
6e7e3d87e101f1fbd995f8c9135664a3 *data/chloroplast.RData
56a106e8143c27252b8588f57ba6f2a3 *data/mites.RData
19f84425e8caaf9f605490cdff17dd81 *data/yeast.RData
e7a4016a58bcd7e93b1bbfa53559b457 *inst/CITATION
61b3722df2ead748e0db8595428412a1 *inst/README
c5e50b084c0fee51feb9c87915fc5c3c *inst/doc/AdvancedFeatures.R
46b7113923dc06e460bf992618388e1a *inst/doc/AdvancedFeatures.Rmd
e53f5a5808b3aadf409ea117d6d5e3f7 *inst/doc/AdvancedFeatures.html
a1acd1e6c375ca1d707f08879a266709 *inst/doc/Ancestral.R
6f34d5bd0b9cbcbaa5752306a6d0176f *inst/doc/Ancestral.Rmd
c782b30836efe480e19c18572823c74c *inst/doc/Ancestral.html
b27a3bfbb0d8cac5db0afb601f91a355 *inst/doc/IntertwiningTreesAndNetworks.R
fe8fb6c254f2f02f37867ab53df0d941 *inst/doc/IntertwiningTreesAndNetworks.Rmd
e07c6553971e517c784eb27608fca6ee *inst/doc/IntertwiningTreesAndNetworks.html
77ce1e05b4f025776bc46baa08378dba *inst/doc/MLbyHand.R
591c6be6c9e5bfcd31b7775346ae1d6c *inst/doc/MLbyHand.Rmd
0ff840256979e575dfa9cafe41c4d7f2 *inst/doc/MLbyHand.html
b406794f68e9b84c00b7018175282526 *inst/doc/Morphological.R
150d4e10a4611040171554e0424d7d56 *inst/doc/Morphological.Rmd
b9dae18a3095c8b6a7866a81f3a76995 *inst/doc/Morphological.html
ed931565687ee9e4ed7fb1e62dd9a2d5 *inst/doc/Networx.R
69f9f3b50e234548e32cf8274cdc1c74 *inst/doc/Networx.Rmd
30234afeac9c004747a176a1b60fd2d9 *inst/doc/Networx.html
da085c25cd1cdde928772bab10e88787 *inst/doc/Trees.R
f6cdcf0f44a3ec84c98cc4e768ae982b *inst/doc/Trees.Rmd
d7065e102f3bf4161abe48272078aa04 *inst/doc/Trees.html
3009f9da02a198cb557d435cc5ad8c7f *inst/extdata/Blosum62.dat
72f496d4c6e937ffe744d25bd8891313 *inst/extdata/Dayhoff.dat
5aa357dab0e72b27023e4302bc37dbad *inst/extdata/FLU.dat
7f63f617d5d29421b0bd90ab8511feb7 *inst/extdata/HIVb.dat
29e1aa10906a86bb9bca6d9c7f98a6cb *inst/extdata/HIVw.dat
ca86e539345fa57de5c77a60308bed09 *inst/extdata/JTT.dat
fdc1176d0c0f2db3de1c9dfd83d3c070 *inst/extdata/MtZoa.dat
106715eba35efc2743ccad7923ac13ce *inst/extdata/RtREV.dat
e05f5a0ca507e4e15e7b95d1ce93b9fa *inst/extdata/VT.dat
fc090d051ce4f18b937448a254e2764e *inst/extdata/cpREV.dat
50c707c26bf9015b37670f15d5e1c14b *inst/extdata/dayhoff-dcmut.dat
6da24109959f0c7a7db50c8db78d5d42 *inst/extdata/jtt-dcmut.dat
ddc4bd45521cd72848aaf2f79b90ac6e *inst/extdata/lg.dat
0102d3cf3cd09ca6360b4d93105f7244 *inst/extdata/mites.csv
3ea55154c033ba80114e345b3d73cf2a *inst/extdata/mites.nex
917303a3df098f9137c651de0afa78fa *inst/extdata/mtArt.dat
1cd5e39670b86d32b5fe5c27dcc79648 *inst/extdata/mtREV24.dat
0ca0d0e987fcebf847a876779eddd934 *inst/extdata/mtmam.dat
b61e63e6b493517a260c904dd902703f *inst/extdata/trees/H3N2_NA_20.csv
e523769910ecbef420758c7a7f252267 *inst/extdata/trees/H3N2_NA_20.fasta
20be734137b889e34006f8b8bd969054 *inst/extdata/trees/RAxML_bestTree.3moles
384aa1b8d633aa8c9f533396bd6798cb *inst/extdata/trees/RAxML_bestTree.AIs
757e4718b72d7829b5ceb34f765dc626 *inst/extdata/trees/RAxML_bestTree.Wang.out
5c7b80221c2dc93d4e6a6b857ccb62e8 *inst/extdata/trees/RAxML_bestTree.YCh
0e77d8f9386ddaee1de2f6678530c823 *inst/extdata/trees/RAxML_bestTree.mtG
2f7670326d5ff9235ecd0943944b6d59 *inst/extdata/trees/RAxML_bipartitions.3moles
959bc9ea585c21ab89b3f32a5bb49d25 *inst/extdata/trees/RAxML_bipartitions.AIs
46c172becde7e1d90ab68820b0c48822 *inst/extdata/trees/RAxML_bipartitions.YCh
75061d3e313e19632dcbce0ef48e9cdc *inst/extdata/trees/RAxML_bipartitions.mtG
2212d49c7269978890887be3686c12f9 *inst/extdata/trees/RAxML_bipartitions.woodmouse
b1b3ceb83427c63fed23790fd563ef6e *inst/extdata/trees/RAxML_bipartitionsBranchLabels.3moles
41fd855853c4ceb7e28d5212b1c72d9b *inst/extdata/trees/RAxML_bipartitionsBranchLabels.AIs
0d8694f8ea078f981819be215fb724ba *inst/extdata/trees/RAxML_bipartitionsBranchLabels.YCh
abcfbaf31212288e26a67c5b6c30ae70 *inst/extdata/trees/RAxML_bipartitionsBranchLabels.mtG
25077ff0b9f822583f5ae13d8bbc181a *inst/extdata/trees/RAxML_bootstrap.3moles
bd830645e73afa0ee2cb121c22c4d2f2 *inst/extdata/trees/RAxML_bootstrap.AIs
086fb65b6bd2d40f09fff513b86d55cc *inst/extdata/trees/RAxML_bootstrap.Wang.out
49ade6ade3f8f08033b887a001243c86 *inst/extdata/trees/RAxML_bootstrap.YCh
d2016de5a6926dd0b62c49502ec2d6b9 *inst/extdata/trees/RAxML_bootstrap.mtG
000df141b844795d38e5a755aa360f97 *inst/extdata/trees/RAxML_bootstrap.woodmouse
6cd945acf5464dce8e10c350097e2c20 *inst/extdata/trees/RAxML_distances.Wang.nxs
02888c45178001387b7a5397a3a17d3c *inst/extdata/trees/Splits.txt
d3069d1eff9e70bed655b8962bf4ee2b *inst/extdata/trees/primates.dna
1caf8878e246688217655fd093a744cf *inst/extdata/trees/seqfile.txt
ed2ca3537729babe51beb1cb41e81dc3 *inst/extdata/trees/tree.txt
129e8c41182f3557b1b9911625e100b9 *inst/extdata/trees/woodmouse.fasta
421488c1ce8687879f64a350fca6d055 *inst/extdata/trees/woodmouse.mrbayes.nex.con
d83fc4958acba1f1d0ca4092393c5b3d *inst/extdata/trees/woodmouse.mrbayes.nex.run1.t
e185a8c9c7aed17a3e216cb78d517fd4 *inst/extdata/trees/woodmouse.mrbayes.nex.run2.t
01399608c5cc2927ebed0659ac78863d *inst/extdata/trees/woodmouse.nxs
87fa1533c4dfe7074237cfa2196bcbeb *inst/extdata/wag.dat
b3ce1bb1450b5e60d76e7e7d9c5db9ce *inst/tinytest/test_Clanistics.R
47e00e8bb86bf7f5c0ee0397941f8cfd *inst/tinytest/test_SH.R
64f06b4775a7662c9966af47ee76f27a *inst/tinytest/test_ancestral.R
35a109c2977b0c0fcb81dd420848d366 *inst/tinytest/test_bootstrap.R
f9882c18bcad5b37772f3162d1136983 *inst/tinytest/test_candidate_tree.R
4fd1391e9729fe532820bcbe2f0a5507 *inst/tinytest/test_codon.R
345ec6007501e54759c9105080aee3f4 *inst/tinytest/test_dist_tree.R
91e058d223bee69969650e223cc0bfa0 *inst/tinytest/test_distances.R
003cf27799c5f9ac3c125e9dbdd94151 *inst/tinytest/test_hadamard.R
40980e23733756c687d4b0bcada09531 *inst/tinytest/test_hash.R
49bec950fdf8ff6034c263a231e3bfe3 *inst/tinytest/test_mast.R
8812a0813225fac2804f9c6ff8714bf1 *inst/tinytest/test_modelTest.R
794b8dffe4ff13605fdf7875fc5d7862 *inst/tinytest/test_parsimony.R
332a6e4bc4dc3be1aa52bde75bd3b3eb *inst/tinytest/test_phyDat.R
5b93808e61220b94c34a2d383aa14293 *inst/tinytest/test_pml.R
6baabdc92fd297936eb619837320ef35 *inst/tinytest/test_pmlCluster.R
d6c4415a1ff82fdc374deccb3f86d2d4 *inst/tinytest/test_pmlMix.R
5f94576ee5e9a927833da9c1bc336a02 *inst/tinytest/test_pmlPart.R
66a962bcc703434a9afff9b4d05168ea *inst/tinytest/test_pmlPen.R
fa168c4f70531e131a617d8462e0bd61 *inst/tinytest/test_pml_generics.R
9fb0c7de01dc40a4eac7d8231c858fa7 *inst/tinytest/test_speciesTree.R
1b7e16921bc9041df2c62f3686721553 *inst/tinytest/test_splits.R
dcac0cc9fbe28aeda00dd6a1bc9f2121 *inst/tinytest/test_superTree.R
91f54f28928a7ce4bc48f00718838e6f *inst/tinytest/test_treeManipulation.R
3645bdd96f541961003448d89470e64e *inst/tinytest/test_treeRearrangement.R
9342744307dbafb5d6db1b02d44a0482 *inst/tinytest/test_treedist.R
9cdc36039e020ffdb6e43c8c75c02d86 *man/Ancestors.Rd
67aeb2d5d5afb5c45bb8580b6db88b99 *man/CI.Rd
2aabd7f30eb4ba55fb913d2defcc8c01 *man/Laurasiatherian.Rd
f0c375eb726b230fdd114f0b3bb1b96b *man/NJ.Rd
5912be549b4f8cee8bf5027d112f697a *man/SH.test.Rd
4e98f950b33245fe670bf81f28ba30bf *man/SOWH.test.Rd
f822ddacf5ef0e1b2ba42fbc1b614e72 *man/add.tips.Rd
ea8d3065732607f6a41c0143e1cd9d77 *man/addConfidences.Rd
9b2205e470fa28e7f7329508815c1cfc *man/add_ci.Rd
62fa559a1d0311fd583a096a08765384 *man/add_edge_length.Rd
6e52ffa9b2657bbd10abb02b2321dcfa *man/allTrees.Rd
bfdd32d75e0bda6b62591a207159a596 *man/ancestral.pml.Rd
2b4c9390c1da5444f929a8db6ab42969 *man/as.networx.Rd
f9afe7e297b97d8e586fc6e7b84dc6c8 *man/as.phyDat.Rd
90bcbd153f4c67d4ff89f4c1501b1515 *man/as.splits.Rd
824c3dc8b4aa39a80aaf0ffe72ee088e *man/bab.Rd
9d76d992214e9f61b11cda0f82f23a76 *man/baseFreq.Rd
2f3e1b465da88336dfc843d2e51c4496 *man/bootstrap.pml.Rd
84449bdbd0b2adefb75bd71de6be5d8d *man/chloroplast.Rd
f787e20d86e0066ef16a220d082241f1 *man/cladePar.Rd
7f22c4b1e1385b67ce4f53b86461bd5e *man/coalSpeciesTree.Rd
42471258d0b98e035383fc6fc48e8665 *man/codonTest.Rd
964ebf567a20fe3bca4154000c576b53 *man/consensusNet.Rd
9a6059134efdbcae3f438ef949806bfd *man/cophenetic.networx.Rd
5173eb8e2f87b21391e5c49c0927e905 *man/delta.score.Rd
157ba81e46af81e8efe4d82e272ed4ad *man/densiTree.Rd
5e47072d5a843c3c8aed0ac39ffa1a2a *man/designTree.Rd
dfbc54435ddc425192da2b8de37a90fe *man/dfactorial.Rd
cebd2eea02c968436b792292842ffb58 *man/discrete.gamma.Rd
571f3efde7105959a3bde517a0f7535e *man/dist.hamming.Rd
8a4bbe826bf261a766136ac74bd13162 *man/dist.p.Rd
bc774bf569c795facda416ce953f5af2 *man/distanceHadamard.Rd
dc442f0a525c0dea47e40ecdab46462b *man/dna2codon.Rd
5e5c9da6e7ba15b472b9ea3958876662 *man/figures/logo.png
5e5c9da6e7ba15b472b9ea3958876662 *man/figures/phangorn_sticker.png
d092f8360372abe2b4fcde6d1b9e3605 *man/getClans.Rd
1b39d04ee91c2585f6a812f683ac2748 *man/hadamard.Rd
b8f30d17d23a015d871b117784492c57 *man/identify.networx.Rd
55fed2375379cf1c518fc59f421d24b1 *man/image.phyDat.Rd
e77fd8dbf4e3b777f4364f88c074fbed *man/lento.Rd
dc624fd67dd7f0146db5b969b8887c06 *man/mast.Rd
502500d11a8c0c44ddc5d53aef6d2523 *man/maxCladeCred.Rd
12f6e2e07e3683dc9adc44fe2678350a *man/midpoint.Rd
3813d65f2d76c7e2b5a8276c44381dc9 *man/mites.Rd
3863a4275711e8fe423a3ed5f8aed588 *man/modelTest.Rd
669667a8bb1230a23708e66338faa5c8 *man/neighborNet.Rd
214b9849369866569e980e7be0bb387a *man/nni.Rd
ac37b43ef6bcab39c7bc29b9fd95ca52 *man/parsimony.Rd
6c6e26bfd7241f125fdbf5c27999e1ad *man/phangorn-internal.Rd
5940c895eff055b18f7df7dccaccaa01 *man/phangorn-package.Rd
c02e3570c26f7140ebd2b386f4e68161 *man/phyDat.Rd
57aaebe7f23aa9d4a08ab3e85b8bc8da *man/plot.networx.Rd
2a2a0a7492f3cd88b978c491b3750192 *man/plotBS.Rd
5f6a6d0605ead49d079e8ae2fc6a9713 *man/pml.Rd
346325ffe2abd76109cbd484a3c64531 *man/pml.control.Rd
f142dfed76d28cf89761bfbbec98295d *man/pml.fit.Rd
750ed9670c8cf38a135a37963597d442 *man/pmlCluster.Rd
e19a5d49ebfbe2b580c2b0d6f8596024 *man/pmlMix.Rd
7a12b0709b9a80537e596db40a1f4216 *man/pmlPart.Rd
a09a6083ee44ca91ebf21588f7c0c073 *man/pml_bb.Rd
f80cfdf44cae9a09939e75d72a4222af *man/read.aa.Rd
d22f32912c219db0ea096add5fe1eb81 *man/read.nexus.splits.Rd
133c5bb904032971f0b5e69afcfe11c9 *man/read.phyDat.Rd
26ad4423a6fd8650b8bf599597615558 *man/reexports.Rd
03065d6d8d2fdbfed0e1fce7561277fc *man/simSeq.Rd
56615aed5311ba4bd692ca7ce6adb1c6 *man/splitsNetwork.Rd
a33948d6c5b8dd8e1ee6fa32e87cdd11 *man/superTree.Rd
a661c6d4a0f5208e1574d8221c28c23f *man/transferBootstrap.Rd
4ccd0c490c4a6e352971180ccda0240f *man/treedist.Rd
73308bbdef266b537f9a6aa413f539b7 *man/upgma.Rd
8d1ad5757e44f5318adabe5b0d94a2e1 *man/writeDist.Rd
7b4fdcfc85bc945a86723f094057dbcb *man/yeast.Rd
427f79cb72f331e85c03454d5af3f8fe *src/Fitch.h
c45a68c7cfa876c9f79acf87d0809a57 *src/Makevars
b1f8a3fd70020ba7cf078bc586eac493 *src/RcppExports.cpp
dc3cbbe97834227fc3ac5456f58848b1 *src/dist.c
a96e879a51643d022766029e97213bb6 *src/dupAtomMat.cpp
59243492d612c0989e8ef4d00be4b6b0 *src/fitch64.cpp
403b0f1d27a423e357f3e96cd7aefe12 *src/lessAndEqual.h
8864a57291c639d781c4684ed924e654 *src/ml.c
6f7f95f69b4d259fdc28d8a87f144fd2 *src/phangorn.c
66922c256930b250098ba2d60e12a6b2 *src/phangorn_utils.cpp
e19952320d4d6bd26c1b95080a7b5d0b *src/phangorn_utils.h
b322aa12ac146cbcdd5d9568a7fdb18b *src/rcSet.h
be65a5e85d58c56ab754b21292ab5360 *src/sankoff.c
1f91da56a713aeb7bf1f0be4a19edadd *src/sprdist.c
3a302c7e7c5126983bbc108aae9b63e2 *tests/tinytest.R
f98f253b2e4d087b4cdc6f7a0819b337 *vignettes/AF.RData
46b7113923dc06e460bf992618388e1a *vignettes/AdvancedFeatures.Rmd
6f34d5bd0b9cbcbaa5752306a6d0176f *vignettes/Ancestral.Rmd
fe8fb6c254f2f02f37867ab53df0d941 *vignettes/IntertwiningTreesAndNetworks.Rmd
591c6be6c9e5bfcd31b7775346ae1d6c *vignettes/MLbyHand.Rmd
150d4e10a4611040171554e0424d7d56 *vignettes/Morphological.Rmd
69f9f3b50e234548e32cf8274cdc1c74 *vignettes/Networx.Rmd
6537f663557a42d79e140b6ad683a329 *vignettes/Trees.RData
f6cdcf0f44a3ec84c98cc4e768ae982b *vignettes/Trees.Rmd
3b1285249eed24e70427c0b56450533a *vignettes/cophylo.png
1ca8b1d97a011a9d0ecd9630d548dfb3 *vignettes/movie.gif
a0c9036e26bf0b3fae480be0ffe40241 *vignettes/phangorn.bib
6b0ad41d4ea31b2e41c1b131c538c69d *vignettes/seqLogo.png
