b15c85c6ff46ee2d46d2775979e64006 *DESCRIPTION
fa2e0cb9ae894adad569bb36a530a11a *NAMESPACE
a2e4e4c4326606e7201e5366344bf4bf *NEWS.md
9b81bbb5b6a0a3de3e57c54909096b46 *R/DNAbin2index.R
134039913e115b9f7326bd9a26f67913 *R/EmptyCells.R
2183becf9e67b8d64e82c0b864b2a4f6 *R/aliscore.R
72f0f63a46f55048475639e383085a3e *R/are.tips.consecutive.R
daf05e512f661941b3c810d17fe47c52 *R/assembleDataNode.R
1125e7a362794975c69e2cf645dc417f *R/assembleDistributionNode.R
cc8eaf6a25f9f07c5529d8c96a6bf7de *R/assembleInitNode.R
086e0c85e9ffa2bb742768f9e0aebe10 *R/assembleLikelihoodNode.R
79b7c550c5be024ebc177d1da30f04ec *R/assembleLoggers.R
ef52ce06b3f9209b9c38666ce7c5304f *R/assembleOperators.R
79b737f49696ae357b93b92dfb421ea0 *R/assemblePriorNode.R
652a82fabf3d09412c30cd5e269f2ab0 *R/assembleStateNode.R
ddebb63de997920dc67c8945efb7952b *R/assembleTaxonSetPrior.R
346c6cfb80e9839b67c5e23118212b02 *R/assembleTreeNode.R
dcbf3ca167bec4d60b7da64e1c777705 *R/beastLog.R
d98bfcfc9aafb12e27382ecbe17f3a9b *R/blastn.R
663c1a3df0ecfe2f86727cc913029aa3 *R/code.simple.gaps.R
765e4a78a6fc2a00f0db6236a943213d *R/collapseUnsupportedEdges.R
8c7bc0b26d3de65d2cb759a81bba9d24 *R/combMyTree.R
85c002377080ed017d669c03f56ce2a8 *R/del.miss.R
b482a0561ff989b65aba7f936b78e18c *R/deleteEmptyCells.R
8c0bea86c48c787785957a79e7f6e8c3 *R/deleteGaps.R
e6a2cc21fe3068862eb510056c176d63 *R/descendants.R
6e405fb14448a81486deac49d4794a95 *R/eoi.R
0377ca904c101238623a2a9217327b00 *R/extractBEASTstats.R
09756f52ea9c8acfe48031c792d0bd6b *R/extractMRBAYESstats.R
976484c2ef7675ed62e7dff415cb8636 *R/findORF.R
53660538d1bb87b2517efe6db58b728b *R/fixNodes.R
202f4604c6bf3414866aab88ed5321f7 *R/forceEqualTipHeights.R
88d530d781edbb7b87ba4f7d56cf9c20 *R/formatSet.R
c1b7e2090064ae5e23aa49eb28e876c8 *R/gammaPrior.R
399d0735d79fc0d26410d2ef7ad8113f *R/gblocks.R
a0b5ce4d147d1a07e4f1cd576054096f *R/identifyEmptyCells.R
911dead0133d5102332e91305e9c0afe *R/index2DNAbin.R
7f050b73753af7589ada17c7a70c74ed *R/mafft.R
1d61e673f1f46ad2fffbfc4765fc4d57 *R/mafft.merge.R
9b9433908f118d7903759ccb3451187c *R/matrixBlock.R
b30a7d69fe91189d6ae87197d39561dc *R/mrbayes.R
9da4ccb8b086cf2319d1133ca1506d05 *R/mrbayes.lset.R
f65b5cc26e691f261008ca2e0f3442a0 *R/mrbayes.mcmc.R
e96f4d51d206b1651f175b3cf93bf100 *R/mrbayes.prset.R
ddde9e33eb56a73acbe91e8f81e8497a *R/multistateMCMC.R
a6296553c6f5b132228f55bac3395092 *R/multistateML.R
67c71f5b4e6370107bdfb5d43c1544b2 *R/neighboringPairs.R
b72daf94be1f6fbc3091d08aaa267774 *R/noi.R
c89194f0e360d0d9a4060435a01f1360 *R/ntip.R
141a36776834b6a761197386360c0be6 *R/oi.R
dcf57be6b58a816f75e946bd7b753c57 *R/operator.R
69854a69c024ed5f752860888b317442 *R/parameter.R
de1c863dc3ca495bfa47ee6ad4860172 *R/partitionfinder.R
0890b3bc379b7009c708c8c1be8e5037 *R/pathd8.R
472692647c1a7d088f8d499928c201d9 *R/phylo2mafft.R
7c14ab2307539d262f827538bbabb2fb *R/phylo2mst.R
1b08149139d8ee5535d74e7e58334c83 *R/pis.R
ccefcb4b6acd95b36cb1fd7c313a2134 *R/prank.R
17d5c1372baaba214aaf0b9167fb221d *R/raxml.R
782e21e5b29cbf05da69cd7b8a6dd687 *R/raxml.partitions.R
c6051094b268dcff1f0ab9573c84d97d *R/rbeauti.R
38e399764626b54c76de6edf1ee7ea2f *R/rbeauti.taxonset.R
652aa54ef213dcf110e4d7565bb2306d *R/rc.R
0d3d90d1161e58e69e2c2852e5a4568e *R/read.R
02eebc6a182853b61d546d8833d3677c *R/read.beast.R
3e79165be3df2deda88ca15031609c9e *R/read.beast.table.R
8757114a3a7ec3796ed3a3d06a49b4fe *R/read.fas.R
b9fd30ed826d9d22772c3d4e04cce87b *R/read.mrbayes.R
c95a15384602be583945a8120e0504e0 *R/read.nex.R
5825be63cee33ebf9eea24dd3044187f *R/read.phy.R
d0510903f1a5296e483fc7dd9d48a15d *R/read.starbeast.R
145e5627ab61b1e96d9d6c64ffca2bf3 *R/read.xml.R
e3c7167348498f382e5a6f0d51e54d6c *R/setClock.R
d4e4a6888e37f126a340d0eac7ed70b2 *R/setMCMC.R
e22230122556155cffc010cae8a44938 *R/sister.R
ba9e13b047a65b8ec7aef15945d1bee8 *R/splitIntoClades.R
8da186bc4d8847aac26bcb116551df05 *R/str2cha.R
c29cf1f415928ab2f103401f4a0c0f8b *R/terminal.clades.R
08ed405c85a0c0432cbafa3f46985930 *R/terminalSisters.R
c79ffdf289063b69dd9f931a59703ea3 *R/tipHeights.R
d3d84db00c844c466826226f9df5969b *R/traitRate.R
76e038bba90acb1b04b0848ae545d629 *R/traitRateOutput.R
33a845fce17eee9b104b21209c3628e6 *R/traitRateParams.R
9953474371a2f3682bbc4c0ecaffe0ee *R/trimEnds.R
8d6e654b5a055412488acf3a4fc14be2 *R/unlistFirstLevel.R
9dde235cb2c3f900f000ce01e7cb6fd1 *R/unresolve.clade.R
bc52a3dae1b881615edcf55339f1220c *R/write.fas.R
b65bc732c49d3efc23b2da9d7d2b23c4 *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
fcc07ffe4af15f69d432aa429c17ffc1 *inst/CITATION
bb305db37667e3a287fadc82b3f49d1c *man/DNAbin2index.Rd
a9902db86f14d9885f1aba2a39bb6dc8 *man/EmptyCells.Rd
43ee5e8fb8f09330b2e37a131ea562ff *man/aliscore.Rd
19e7f6ae9210a3aa0a3a1ea80080cebc *man/beastLog.Rd
8b14fc95a5aeb132f79fe1346d9095b1 *man/blastn.Rd
7dece938e6277b9ac876070aac14f648 *man/code.simple.gaps.Rd
22872f37dad0a63cbf1aa703445dba5b *man/collapseUnsupportedEdges.Rd
6e2189b2216ea8187850c6480d5c437b *man/combMyTree.Rd
f5052cc32a353614dc191b8280c5a0a9 *man/del.miss.Rd
1fc8e3926864b87f00e642c2f3e40c60 *man/deleteGaps.Rd
666e59318f52ff2c3dfcfa03bc0b1f0b *man/descendants.Rd
2e0df90140b417ceed13b9bf72a92148 *man/fixNodes.Rd
6f31a2dc6b6d568b63174033812ed4e1 *man/forceEqualTipHeights.Rd
6e1dca69cda8176854d9889dadc8ebc9 *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
c4997bc77bab4fb2c93b21eb4bb395c2 *man/mafft.merge.Rd
6157bad16cfc78776906613c4c95b31e *man/mrbayes.Rd
e5d6557e5abb02e54771aacb3bef91bc *man/mrbayes.lset.Rd
d693da70dd22c04e596452a8a35079de *man/mrbayes.mcmc.Rd
89203dc545e9ba4c28e780a292a4ee83 *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
6e54e4712e5e41f9e5fac36ea1269c2d *man/raxml.partitions.Rd
2f567ce134f5fbee4a9a20f41c7cd84f *man/rbeauti.Rd
dfb2ff016f82b91d23f6ee7b951878e9 *man/rc.Rd
351df92063bae71f0647d692cfaf2c11 *man/read.Rd
6cfa32787dd049ddaadf3534b633713f *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
