647fa48e9e4f712b7b9ba01551f8b9ab *DESCRIPTION
fa2e0cb9ae894adad569bb36a530a11a *NAMESPACE
bf3c0c55fb661e0815111766561662a4 *NEWS.md
9fa310bc86842288bf388cadd7335bcf *R/DNAbin2index.R
eb771266c4aa868ded064aae10003c85 *R/EmptyCells.R
e29236f16815d1d3bb4415054ef1085f *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
865fb8065eb75b4ca27b1bb981f0ba2c *R/collapseUnsupportedEdges.R
b1941318869b35ca04c3a0ca63d93619 *R/combMyTree.R
b410e0bdb1c5c29ae5620b17268b1756 *R/del.miss.R
b482a0561ff989b65aba7f936b78e18c *R/deleteEmptyCells.R
f5a6dfc41f04430525811dee94554c14 *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
4e4dccfe756f96547bc454b4cf5b7ef8 *R/forceEqualTipHeights.R
88d530d781edbb7b87ba4f7d56cf9c20 *R/formatSet.R
c1b7e2090064ae5e23aa49eb28e876c8 *R/gammaPrior.R
0e3f6919f717db32e800602ce23e8aa7 *R/gblocks.R
a0b5ce4d147d1a07e4f1cd576054096f *R/identifyEmptyCells.R
541c22be3fd0b1cc9f25ba2ef340c5d6 *R/index2DNAbin.R
5a69ec2528b507df01aee4b08fff8da1 *R/mafft.R
d0964843d76f7662ea244796f4c4da12 *R/mafft.merge.R
9b9433908f118d7903759ccb3451187c *R/matrixBlock.R
9535f0bc5c4a6cbe563c5b351c1a0f84 *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
d3b9c259a93eb5bf13d74b818e972a1c *R/neighboringPairs.R
b72daf94be1f6fbc3091d08aaa267774 *R/noi.R
1a9a21474e9628c17af3e5428f845d63 *R/ntip.R
a3f4d5e04f8e027704f21fa923645b37 *R/oi.R
dcf57be6b58a816f75e946bd7b753c57 *R/operator.R
69854a69c024ed5f752860888b317442 *R/parameter.R
de1c863dc3ca495bfa47ee6ad4860172 *R/partitionfinder.R
c9370b7f89d183a92801e6c1c9f71101 *R/pathd8.R
45cadecb2216eef9210db68bb25d1459 *R/phylo2mafft.R
d1b6be6097c8c04c20fd9ec92fef2e05 *R/phylo2mst.R
db1067ebe544ace09c658227bb2efcf7 *R/pis.R
ccefcb4b6acd95b36cb1fd7c313a2134 *R/prank.R
7d9b53c3317fb9148eb9c8a67cdf9940 *R/raxml.R
782e21e5b29cbf05da69cd7b8a6dd687 *R/raxml.partitions.R
e10caa1c11387ac8e7cab92bf56b5c13 *R/rbeauti.R
38e399764626b54c76de6edf1ee7ea2f *R/rbeauti.taxonset.R
652aa54ef213dcf110e4d7565bb2306d *R/rc.R
88428a9c2fe8e16e967c11a86a62e7ca *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
8d6d9aac8944a96b42546a188d3d7dd6 *R/sister.R
7e47cd56c29d31e1ab2cea818df7a1f6 *R/splitIntoClades.R
8da186bc4d8847aac26bcb116551df05 *R/str2cha.R
c29cf1f415928ab2f103401f4a0c0f8b *R/terminal.clades.R
921baf702e6a0709b939e5741a7641fd *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
f3d1840e7c194d47381faecb18bb9d14 *man/DNAbin2index.Rd
dfc9b156c8bf941390d3b08eedbc17e9 *man/EmptyCells.Rd
adf592eab887d8a97cb677e8ae881c17 *man/aliscore.Rd
19e7f6ae9210a3aa0a3a1ea80080cebc *man/beastLog.Rd
8b14fc95a5aeb132f79fe1346d9095b1 *man/blastn.Rd
9f2ef108858922d8cf8538394745bde4 *man/code.simple.gaps.Rd
ee450c058ac0b379f641a1e709db811d *man/collapseUnsupportedEdges.Rd
53178bd2c8a98737dfdaf04cf30db26f *man/combMyTree.Rd
e2029e1f3ba9659bfbe4dbccc11da8b3 *man/del.miss.Rd
4f6a8bf187146de994e2cbf9b5eaeee2 *man/deleteGaps.Rd
26db9fa581be376fc1891a5673ed35a7 *man/descendants.Rd
6f66dc17f37bb93ae58f1a2a58690a02 *man/fixNodes.Rd
45356505ad06a0ff3a59d28458d60f5e *man/forceEqualTipHeights.Rd
874ea453785fe9f919da370ecc24966c *man/gblocks.Rd
a7c5e1e3e0d6b14bbb44089ab37d1d5e *man/index2DNAbin.Rd
f04ad9c579a3b3bc28ff1d7065d713ae *man/ips-internal.Rd
483fd85aaf79e29b45e470a38f397e55 *man/ips-package.Rd
4f49dbc483d2bff91ce0d6a57f1014d9 *man/ips.16S.Rd
ebeb6900a79c9701d6d6bcfcbbb512fc *man/ips.28S.Rd
3191cf34114ea41d2f779b44ed8a828a *man/ips.cox1.Rd
d61b8215f1fc67e7bf66a0ec387a97bb *man/ips.tree.Rd
9caeabbc2bb05802981efffb555e34b2 *man/mafft.Rd
de1d3cb8618dfa7f629d9c68ec41bb28 *man/mafft.merge.Rd
824c3a8a5e385763bbddb1d85a689e8d *man/mrbayes.Rd
e5d6557e5abb02e54771aacb3bef91bc *man/mrbayes.lset.Rd
d693da70dd22c04e596452a8a35079de *man/mrbayes.mcmc.Rd
89203dc545e9ba4c28e780a292a4ee83 *man/mrbayes.prset.Rd
8d700177a0c2a8c923d7dba7bc883425 *man/multistate.Rd
3f87c033036086b551c231b9a03d74a6 *man/neighboringPairs.Rd
ec43da38f46143147c3f47bc1a0f674d *man/ntip.Rd
d879fc8ca1b93f1ec29203cf04ded947 *man/oi.Rd
17c20b5d2043b63735ddae89a29bb5fb *man/partitionfinder.Rd
0ba4db056bc1f021bc0bbf86d746a534 *man/pathd8.Rd
7312f156b8562c519bee49d830f0d7b4 *man/phylo2mafft.Rd
813bd9f6d87b77be6d9c326ed46b53bf *man/phylo2mst.Rd
13461bc2aa733337a51dddcfa1e4450f *man/pis.Rd
19f9e064eaef29e5829a5b2c9298caaa *man/prank.Rd
da329b536df9b78cc14099f816e3d61f *man/raxml.Rd
aeb036b30279dbdebd89ed419bd833c0 *man/raxml.partitions.Rd
3d7ff76d55cfbaef47bcd429e2402647 *man/rbeauti.Rd
dfb2ff016f82b91d23f6ee7b951878e9 *man/rc.Rd
1203bea2ab1b174725ada41050f5d1ce *man/read.Rd
6cfa32787dd049ddaadf3534b633713f *man/read.beast.Rd
f3300894cd05b3208b744a9260c5cd6d *man/read.beast.table.Rd
1a27c9b3995ce6772cc0013faf562719 *man/sister.Rd
2f03e0a046b897de502bc509e5975964 *man/splitIntoClades.Rd
49d2abc4f2ec661c6e99f330e31f1f74 *man/terminalSisters.Rd
126f1a2480f1902e9075e099a7cbbd1d *man/tipHeights.Rd
f19ba309da90fa24f3fbd31d5f094773 *man/traitRate.Rd
ddebaa6e8d93602f7be974f329afb4ac *man/trimEnds.Rd
12c95930bf2ded955567bbbd59012ed2 *man/unlistFirstLevel.Rd
06aacfa8451abf9b90326f853b288da3 *man/write.fas.Rd
