248b3b1825084ef7b9d282f28a973e36 *DESCRIPTION
8f836f365572854b8d0edb64f557cc3c *NAMESPACE
9fa310bc86842288bf388cadd7335bcf *R/DNAbin2index.R
2069685753836750b43e63f30f9f631f *R/aliscore.R
72f0f63a46f55048475639e383085a3e *R/are.tips.consecutive.R
ad5b54bc96536132eb8b047ea4570fa6 *R/assembleDataNode.R
9b4dd465045579882d2fe44ee2e3e917 *R/assembleDistributionNode.R
812d1b535d17ba38ad96c2dccd00a4c8 *R/assembleInitNode.R
62086a747b5e09da6c362f4ca624f7e8 *R/assembleLoggers.R
63eb0ed2e45315c9a7a62309beb779cf *R/assembleOperators.R
e9c17b7abbf66fc345ce2989acdcbcf2 *R/assembleStateNode.R
663c1a3df0ecfe2f86727cc913029aa3 *R/code.simple.gaps.R
865fb8065eb75b4ca27b1bb981f0ba2c *R/collapseUnsupportedEdges.R
b410e0bdb1c5c29ae5620b17268b1756 *R/del.miss.R
7537b2d07140ce8d39bcc86d02980bf8 *R/deleteEmptyCells.R
f5a6dfc41f04430525811dee94554c14 *R/deleteGaps.R
f861acc438d4f5ce6d51f91ef9a3c113 *R/descendants.R
6e405fb14448a81486deac49d4794a95 *R/eoi.R
93310a46a9e9884ee1b3a97b555b12b6 *R/extractBEASTstats.R
09756f52ea9c8acfe48031c792d0bd6b *R/extractMRBAYESstats.R
976484c2ef7675ed62e7dff415cb8636 *R/findORF.R
53660538d1bb87b2517efe6db58b728b *R/fixNodes.R
4e4dccfe756f96547bc454b4cf5b7ef8 *R/forceEqualTipHeights.R
88d530d781edbb7b87ba4f7d56cf9c20 *R/formatSet.R
e33b756adfea0769f831a0c5295a0393 *R/gblocks.R
541c22be3fd0b1cc9f25ba2ef340c5d6 *R/index2DNAbin.R
2dad87c31a4454ef4d96b2343bb12b78 *R/mafft.R
d0964843d76f7662ea244796f4c4da12 *R/mafft.merge.R
9b9433908f118d7903759ccb3451187c *R/matrixBlock.R
67cf1d13d939389c8e20c32ef07fb92c *R/mrbayes.R
9da4ccb8b086cf2319d1133ca1506d05 *R/mrbayes.lset.R
f65b5cc26e691f261008ca2e0f3442a0 *R/mrbayes.mcmc.R
e96f4d51d206b1651f175b3cf93bf100 *R/mrbayes.prset.R
ddde9e33eb56a73acbe91e8f81e8497a *R/multistateMCMC.R
ce64b66af790f26dde060380c72a6673 *R/multistateML.R
d3b9c259a93eb5bf13d74b818e972a1c *R/neighboringPairs.R
b72daf94be1f6fbc3091d08aaa267774 *R/noi.R
1a9a21474e9628c17af3e5428f845d63 *R/ntip.R
a3f4d5e04f8e027704f21fa923645b37 *R/oi.R
de1c863dc3ca495bfa47ee6ad4860172 *R/partitionfinder.R
c9370b7f89d183a92801e6c1c9f71101 *R/pathd8.R
8487a53e1cd99380bfc5c0c779f77eac *R/phylo2mafft.R
d1b6be6097c8c04c20fd9ec92fef2e05 *R/phylo2mst.R
fba17ad7c8b4ac1ada7c14aafcfce3ed *R/pis.R
3a0efc294f63c9087a8792a21d6a434d *R/prank.R
e13ea4180f7b388ea76cb400f6afe8bf *R/raxml.R
782e21e5b29cbf05da69cd7b8a6dd687 *R/raxml.partitions.R
5ac326ee3bd7f7cab78752bc30ede38e *R/rbeauti.R
ffd2db46f7ebca15dccc0ddfb5451c42 *R/rbeauti.taxonset.R
05fbfd3330a240754f55166ae9b4489e *R/rc.R
88428a9c2fe8e16e967c11a86a62e7ca *R/read.R
53ef6b99392845d1c6f1191914c49efb *R/read.beast.R
1e70dbe21736facefe6afb2e23090018 *R/read.beast.table.R
7453bd398bdafba652996c1301571d3e *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
848e15c64400f3e3d80d64c568a3752b *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
d8e3f906c417f7e4037c5fdc4d9e9edd *R/trimEnds.R
8d6e654b5a055412488acf3a4fc14be2 *R/unlistFirstLevel.R
9dde235cb2c3f900f000ce01e7cb6fd1 *R/unresolve.clade.R
bc52a3dae1b881615edcf55339f1220c *R/write.fas.R
d467002b4385ea374d6e56256c78c266 *R/write.nex.R
b26692c4387891a6bf0bd79ee1d6d569 *R/write.phy.R
ff50ebb531137c2dc18f913dee0bc9b2 *README.md
e0947f2711537bf8dd79622fb5b083b1 *TODO
58f814b5ad2213dd833f46c44370a852 *data/ips.16S.rda
2446bd3b9dbc873d99e8b1b4136e7c62 *data/ips.28S.rda
6ae42a72bdba72d6cf819d218b3e6ad2 *data/ips.cox1.rda
d4479884804c74cb06228ba887d771e9 *data/ips.tree.rda
b54cd3bcf91bdeb8f652068f974ae7eb *inst/CITATION
09685e79138bf4a0f0b5081a4f15358c *inst/NEWS.Rd
f3d1840e7c194d47381faecb18bb9d14 *man/DNAbin2index.Rd
ac30ad2936e4ca3084e701a049e3c87f *man/aliscore.Rd
9f2ef108858922d8cf8538394745bde4 *man/code.simple.gaps.Rd
ee450c058ac0b379f641a1e709db811d *man/collapseUnsupportedEdges.Rd
e2029e1f3ba9659bfbe4dbccc11da8b3 *man/del.miss.Rd
db77091ed9f74d4d53eb86a64ec251a2 *man/deleteEmptyCells.Rd
4f6a8bf187146de994e2cbf9b5eaeee2 *man/deleteGaps.Rd
26db9fa581be376fc1891a5673ed35a7 *man/descendants.Rd
6f66dc17f37bb93ae58f1a2a58690a02 *man/fixNodes.Rd
45356505ad06a0ff3a59d28458d60f5e *man/forceEqualTipHeights.Rd
26a709e369a1c774a31fa91a204b479b *man/gblocks.Rd
a7c5e1e3e0d6b14bbb44089ab37d1d5e *man/index2DNAbin.Rd
7fa357c786ac9134fe9ad85ff5d4827d *man/ips-internal.Rd
6df04723bd657a5535ee711d4e2e4de8 *man/ips-package.Rd
80e2c4ae8636f39af2f8d6d30dcb944c *man/ips.16S.Rd
633716d2ca213e8b2bc876849bab3a93 *man/ips.28S.Rd
b474eee40d95f6d2f5b165ca06eda99b *man/ips.cox1.Rd
8bda7f2fa01c084d1ce58acf9e4f22b9 *man/ips.tree.Rd
8404970b7d665f656cba61d3eeaefd5b *man/mafft.Rd
b929df5596bdc0fe13fc80e3ada759da *man/mafft.merge.Rd
87b9382d03367e2d831c1e5106534c4d *man/mrbayes.Rd
fb69f3c6d21bcab0f438ee3fe82cb642 *man/mrbayes.lset.Rd
b9f1fdf39af5ee5ae7fea71ef44b5b67 *man/mrbayes.mcmc.Rd
33a19c0efb76140d68f83667453946f2 *man/mrbayes.prset.Rd
b1fb03143726c09dce45d95fabd2ae1b *man/multistate.Rd
3f87c033036086b551c231b9a03d74a6 *man/neighboringPairs.Rd
ec43da38f46143147c3f47bc1a0f674d *man/ntip.Rd
2c1a38f8b7993cbcaf0170cfc97c9377 *man/oi.Rd
cef83a55cdaf892c0ad1c29c86e57e4e *man/partitionfinder.Rd
0ba4db056bc1f021bc0bbf86d746a534 *man/pathd8.Rd
994d836d88674841479399430d15e1f6 *man/phylo2mafft.Rd
813bd9f6d87b77be6d9c326ed46b53bf *man/phylo2mst.Rd
878d2062c5030c242b820b48382c714c *man/pis.Rd
418dca42cb0bf995d9dd0d730bdea7ec *man/prank.Rd
4edf2dee7b0a69080731315d34b7683a *man/raxml.Rd
aeb036b30279dbdebd89ed419bd833c0 *man/raxml.partitions.Rd
a5f068d3a618a5adf33bffb3e2e5234a *man/rbeauti.Rd
1203bea2ab1b174725ada41050f5d1ce *man/read.Rd
43fabc7fe9ecc7eb432f27a8071241b9 *man/read.beast.Rd
784715fa25769650751efea5bde7dfa0 *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
