508861c0e7b206e3dba21f41ab11eb36 *DESCRIPTION
6cf13f88dda9b5a4ac2bc0957a75cb0c *NAMESPACE
60e9a6eb3bf8b053333b4c95228564af *NEWS.md
e87b014e699cf40558de6dfbdb12ead5 *R/DNAbin2index.R
8cf85c98739fc66692d7698ca57ae886 *R/EmptyCells.R
1b5fc050b1283799faa7bea33524bddd *R/aliscore.R
ebcd36d81485f0cb3a8792a299be4ff4 *R/aperm.DNAbin.R
2cf8b3308026d25b387327b48e03bf0c *R/are.tips.consecutive.R
e05017278b545a460ef3806bf66f8fc8 *R/assembleDataNode.R
39b5fe2dc4e8f442bb35e55c7faec144 *R/assembleDistributionNode.R
40432fa5204648757fd3f8129abd6c05 *R/assembleInitNode.R
086e0c85e9ffa2bb742768f9e0aebe10 *R/assembleLikelihoodNode.R
ecdbd66ca7011f0bf4d134b9f782f9ee *R/assembleLoggers.R
cc19317fe13c525eaf9b08ef61a996ee *R/assembleOperators.R
79b737f49696ae357b93b92dfb421ea0 *R/assemblePriorNode.R
7f0a6fe5849b343a4ede8e4722f78b26 *R/assembleStateNode.R
ddebb63de997920dc67c8945efb7952b *R/assembleTaxonSetPrior.R
346c6cfb80e9839b67c5e23118212b02 *R/assembleTreeNode.R
dcbf3ca167bec4d60b7da64e1c777705 *R/beastLog.R
3365ffa2da966cfacd12abb4bac18dfd *R/blastn.R
0f47ea1cf26035c5877d29b6735a327c *R/code.simple.gaps.R
b6635647722950f59f262190257391d6 *R/collapseUnsupportedEdges.R
97b575d58cb55dfe132554304c6fb2c6 *R/combMyTree.R
fc5cb92803f69ee38377144d27c8ff19 *R/del.miss.R
85344202378a8c28ed274100a18a579a *R/deleteEmptyCells.R
94b9a80f478760b002302593e5f05c97 *R/deleteGaps.R
9cb825c884b8540787ac0a6dbe2c749f *R/descendants.R
6e405fb14448a81486deac49d4794a95 *R/eoi.R
0377ca904c101238623a2a9217327b00 *R/extractBEASTstats.R
09756f52ea9c8acfe48031c792d0bd6b *R/extractMRBAYESstats.R
976484c2ef7675ed62e7dff415cb8636 *R/findORF.R
3180fe733044e3214887c45537f9273e *R/fixNodes.R
c0690ba8bd82f2ccc78242abb9215e15 *R/forceEqualTipHeights.R
0baa201fab6265f5846a248c80f05dfc *R/formatSet.R
c1b7e2090064ae5e23aa49eb28e876c8 *R/gammaPrior.R
68c6b059fc5cd93e3baed4bb2b5547c7 *R/gblocks.R
a0b5ce4d147d1a07e4f1cd576054096f *R/identifyEmptyCells.R
b8f5fa081259e6dba117547e14aecae4 *R/index2DNAbin.R
1b4c955c6dda0707cbd8cb6c16928a60 *R/mafft.R
1fcba68a95b61314422b9f9c6dab1387 *R/mafft.merge.R
65dc54de9a2f4e3e50780e84be0eae8c *R/matrixBlock.R
025846e24cb4452950b6fcc1c2e5d84e *R/mrbayes.R
017afbbcb363998247fdeee51bf7ca84 *R/mrbayes.lset.R
cc7424c3ada8a0d1197b45c2b8726809 *R/mrbayes.mcmc.R
b12075c74e324f6aee65a3681def2e7b *R/mrbayes.prset.R
1481e899ec2e935936be1a6d35c81714 *R/multistateMCMC.R
f8dffe3d71b3647c0309689e459464bc *R/multistateML.R
389b2cdafd08a50ebd55485b1f4fb1b7 *R/neighboringPairs.R
da181241987b17d28d5f52c35690e837 *R/noi.R
8f81f5deef114ce74fc821ec1dcb2643 *R/ntip.R
141a36776834b6a761197386360c0be6 *R/oi.R
dcf57be6b58a816f75e946bd7b753c57 *R/operator.R
69854a69c024ed5f752860888b317442 *R/parameter.R
de1c863dc3ca495bfa47ee6ad4860172 *R/partitionfinder.R
0890b3bc379b7009c708c8c1be8e5037 *R/pathd8.R
233f018d24f988fcef5354f01d086d11 *R/phylo2mafft.R
ec995e6b2be9d69bbcfc13f03bea304d *R/phylo2mst.R
09038c94d8ac241c2a486bf4392af120 *R/pis.R
989073926c923c8d000beb1572964e34 *R/prank.R
e5d371221d4b484847ee2da170619a54 *R/raxml.R
248783a8c28ee47379210550ada476c3 *R/raxml.partitions.R
002e294a6af23fb4ddd7c537fc69d19b *R/rbeauti.R
38e399764626b54c76de6edf1ee7ea2f *R/rbeauti.taxonset.R
b3856ad22a1b283041cabefb983b7574 *R/rc.R
0d3d90d1161e58e69e2c2852e5a4568e *R/read.R
e3d0daeeaee0425310dfad72c685bd99 *R/read.beast.R
3e79165be3df2deda88ca15031609c9e *R/read.beast.table.R
6c0dffc4c78b994613725713492b7b7b *R/read.fas.R
0de3fb8ee0941408c69af14476e87d71 *R/read.mrbayes.R
98bfa62137d9eb13e2da1da6675be7bc *R/read.nex.R
8002773b5b3ffb8da672058869a6925c *R/read.phy.R
863c3a264eab7aba17962efb3085290b *R/read.starbeast.R
a2c17f02f9dcc825bc63bd18edcfa376 *R/read.xml.R
1acb0993a82d176e9813e0db974010a9 *R/setClock.R
6ea877c800cbc3143eae5ebc15b82a43 *R/setMCMC.R
71d1ef4ac7b1a903d13e4205299fc7e3 *R/sister.R
861ba4e260719e54edef5c0fead04a04 *R/splitIntoClades.R
c55e8b352ac6991ccfb3fc726a2005e7 *R/str2cha.R
c29cf1f415928ab2f103401f4a0c0f8b *R/terminal.clades.R
dfbad342a120d138201b0e3a9fb75964 *R/terminalSisters.R
f93478bacd55aed17f7511f27ddf15d1 *R/tipHeights.R
1c12a5541c0c36e7f844e40f54f5de6f *R/traitRate.R
76e038bba90acb1b04b0848ae545d629 *R/traitRateOutput.R
33a845fce17eee9b104b21209c3628e6 *R/traitRateParams.R
61e4de32207e0cfcb991efc828e2fb8c *R/trimEnds.R
8d6e654b5a055412488acf3a4fc14be2 *R/unlistFirstLevel.R
966a228559e60273a0deb1a57342bf79 *R/unresolve.clade.R
90da17de267eef29487853a5f1623a04 *R/write.fas.R
e72e360984612e91b4e515393c9699c6 *R/write.nex.R
b26692c4387891a6bf0bd79ee1d6d569 *R/write.phy.R
030a2a972525ccb72b942297fee59552 *README.md
e0947f2711537bf8dd79622fb5b083b1 *TODO
58f814b5ad2213dd833f46c44370a852 *data/ips.16S.rda
2446bd3b9dbc873d99e8b1b4136e7c62 *data/ips.28S.rda
6ae42a72bdba72d6cf819d218b3e6ad2 *data/ips.cox1.rda
d4479884804c74cb06228ba887d771e9 *data/ips.tree.rda
00d60fa5276db666043152e4d97aa838 *data/log_list.rda
be066fa210f4a99b0d96dfdbefa6a45c *data/operator_list.rda
47b84d2cb6c7cbec46e46575876cf2f0 *inst/CITATION
074002f1389043543744d03cb6d87615 *man/DNAbin2index.Rd
140e8f2c61d94ac45c650041bb5d1983 *man/EmptyCells.Rd
a7a47ad26b7876f4073de2a71607f070 *man/aliscore.Rd
52f301fed318c28fa64b59ed206aebee *man/aperm.DNAbin.Rd
19e7f6ae9210a3aa0a3a1ea80080cebc *man/beastLog.Rd
8b14fc95a5aeb132f79fe1346d9095b1 *man/blastn.Rd
7dece938e6277b9ac876070aac14f648 *man/code.simple.gaps.Rd
3c0e64f6be7ee19e600b939ee357cf05 *man/collapseUnsupportedEdges.Rd
a84db6549cdc05705311bcbd543d1937 *man/combMyTree.Rd
f5052cc32a353614dc191b8280c5a0a9 *man/del.miss.Rd
1fc8e3926864b87f00e642c2f3e40c60 *man/deleteGaps.Rd
666e59318f52ff2c3dfcfa03bc0b1f0b *man/descendants.Rd
21e9565259c9ca06a249d62178739ca9 *man/fixNodes.Rd
6f31a2dc6b6d568b63174033812ed4e1 *man/forceEqualTipHeights.Rd
767ce4431f6605ca1f8160cc3b7ce050 *man/gblocks.Rd
6769d9e8bca79a4bf4512654413d447e *man/index2DNAbin.Rd
f04ad9c579a3b3bc28ff1d7065d713ae *man/ips-internal.Rd
d955b5a3ef1c56c544cb2175465bc3ef *man/ips-package.Rd
687e9c766c73f989ed158d0eefafdc65 *man/ips.16S.Rd
58796c95462a564eabbc0517b8d4bdd3 *man/ips.28S.Rd
374eb590bfb4cfb8ee5435e69a9cf9fa *man/ips.cox1.Rd
d61b8215f1fc67e7bf66a0ec387a97bb *man/ips.tree.Rd
7cf6e1b88f8743422ccf9a0f1fa6c5ff *man/mafft.Rd
22732bf54cdc9fc1a78cefcb0249a216 *man/mafft.merge.Rd
edb3a98f98123ce6491c265b2521aa2f *man/mrbayes.Rd
7f3e44faf440f9113ac607c1dfaedb15 *man/mrbayes.lset.Rd
dd4b34409f840511b28e8c33d693a5aa *man/mrbayes.mcmc.Rd
a288e0e0fe63cadbf856947c9409a7eb *man/mrbayes.prset.Rd
82690b298e4bbb5c19a2f67b19668792 *man/multistate.Rd
ab609af0f8200d1f03306dd6c27a8484 *man/neighboringPairs.Rd
0597250840c08be176d45fc333091c5f *man/ntip.Rd
1e55e37abbed8dcd922c839e1a93aae2 *man/oi.Rd
17c20b5d2043b63735ddae89a29bb5fb *man/partitionfinder.Rd
e2bb9d10203e8ae245682f7548f07950 *man/pathd8.Rd
0a0e3865cc9ffc283f9e31699cf1847c *man/phylo2mafft.Rd
8aa77bc4fb38d9541afb7739a6f794b7 *man/phylo2mst.Rd
9d0da70d1e68ebb7fb9be02e4a0faad8 *man/pis.Rd
19f9e064eaef29e5829a5b2c9298caaa *man/prank.Rd
9dc628291cd7fb2515ac6ff246418f53 *man/raxml.Rd
179bdd2cfb10fae3f065b69ae497ab56 *man/raxml.partitions.Rd
abd1b01f5df7c6f32ee06c17cae01b6d *man/rbeauti.Rd
dfb2ff016f82b91d23f6ee7b951878e9 *man/rc.Rd
351df92063bae71f0647d692cfaf2c11 *man/read.Rd
19583d65156d832d2960841123d92bf7 *man/read.beast.Rd
f3300894cd05b3208b744a9260c5cd6d *man/read.beast.table.Rd
497295f21cb6b9bcd2dcc47e02072ce2 *man/sister.Rd
018514c5aab8c3646ad3445d1c5c8991 *man/splitIntoClades.Rd
c04bb13b95f5eecf71ce86d8ef559cbd *man/terminalSisters.Rd
73b468e64f64f4816f1f1a225c25629e *man/tipHeights.Rd
f5aa14b2aad95bbf731b4fc231482e4e *man/traitRate.Rd
ddebaa6e8d93602f7be974f329afb4ac *man/trimEnds.Rd
12c95930bf2ded955567bbbd59012ed2 *man/unlistFirstLevel.Rd
359662e21439c539c22b8168dde3b1f1 *man/write.fas.Rd
