2fbe90125dbfbd220c498bd38530f278 *DESCRIPTION
2391513b443364e8920a2d1d05bb2234 *NAMESPACE
7a2ccffedc323ad9f02d0058fad013f7 *R/Alphabet.R
ecd0f4e87dd8dcaab69a7dfea507c002 *R/AminoAcidMatrices.R
42817e81da280a2ede6d0010fb963def *R/AminoAcidSubst.R
c187a9bde2ef3ab4eadc8c4a304af0fa *R/BinarySubst.R
652347048cfdbbb71074e00555530cbf *R/BrownianInsertor.R
6eaaa18af82b334c6b8c80d362151ad3 *R/CodonAlphabet.R
a111e10ab32c1aa53a80a6e2d5298aa1 *R/CodonModels.R
c577e97f2369159f3f6fff6c49024a82 *R/CodonSubst.R
8657b4e727b44b1a6beb7c81fb687ca1 *R/ContinuousDeletor.R
2c247b42b7024a70da622cdfdd709049 *R/ContinuousInsertor.R
d6994f94aea6d6b6ab04641e545b1e48 *R/DiscreteDeletor.R
bb26d26ef684625cabef84122a414c67 *R/DiscreteInsertor.R
573f576ebecb1454677272c39d8f6cfd *R/EmpiricalCodonMatrices.R
ce4ac1945618478e7c4525ea53c19c68 *R/Event.R
0a13cbd294830ea9e009de61d5382049 *R/FieldDeletor.R
a23736811e89e9bdda791d2d2ec6c5dc *R/GeneralInDel.R
380b709d56b8cffa6c8c75ed09d8feba *R/GeneralSubstitution.R
a57f893884e0be7e723de922a49a236a *R/NucleotideModels.R
7e97fdd11f1160a8451c0e4031fbb521 *R/PSRoot.R
6a96f0bde221101978ea5953b8b0da9e *R/PhyloSim.R
5d0ff975e23af341f5a60ae170a7e16d *R/PhyloSimSource.R
41fed7e08543ca1a56f2ac6b98f4e3c7 *R/PopularAlphabets.R
6821e9a7ee91c7c07fea41310d758e69 *R/PopularSequences.R
5b3179fa03bac87babc2922c58e0172c *R/Process.R
34d092f1008c1bdc67fccc57dd7988c3 *R/QMatrix.R
a7eb62562d31ceb10471d1ac1d6698f7 *R/Sequence.R
5b0b67c8a6b3b43bb264f22def9d7632 *R/Site.R
12d6e28abe9a7bd5653026405a15ef3d *R/ToleranceSubstitution.R
62e8d71dff1a26f68be3c692b7d2cdef *build/vignette.rds
0f0bd1cf633ed71d158fc079ebbf2d43 *data/ECMrest.RData
b770273c568db3f69c2851c6e4aff037 *data/ECMunrest.RData
54768f73dbdf171ccf153b2190e1bc45 *data/JTT.RData
5c94aca957e9473077dd34bf6a0e74ac *data/JTT.dcmut.RData
43fb4950a7377fd0486fb8188240a58a *data/LG.RData
b61a191e85b2a92315fd74904539530e *data/MtZoa.RData
be0cf93ecbe04ac54e1cda195d5c81ed *data/PAM.RData
dda26784eac59c9b5f831fdfd0e7d933 *data/PAM.dcmut.RData
01573ee2b7db8cafcad7f9606bcff9ae *data/WAG.RData
819b5956d4e73adc496d53761e79c481 *data/cpREV.RData
07a5d6fce2276d4bc7b64d7438e21067 *data/mtArt.RData
e787aaa1544ddd716e6213e6fa84214c *data/mtMam.RData
ed833396a7ac871be3ccd2c6366dd079 *data/mtREV24.RData
8684a6b77561352afcf31fb104a62988 *inst/doc/PhyloSim.R
1d3e687aec2e6c74f84ddc3dd9af7931 *inst/doc/PhyloSim.Rnw
33588164bb3435fd4cd669e2dc5b87b7 *inst/doc/PhyloSim.pdf
0dba12935ac2b301d839d7063bd6c810 *inst/extdata/ECMrest.dat
ab158a04dcf80310282b7f5c344531ee *inst/extdata/ECMunrest.dat
c0582b4193e3d35d748d8f6d90b305cf *inst/extdata/MtZoa.dat
61a899bae16d1eeba9a77b5f8a7a1783 *inst/extdata/cpREV.dat
f1326e01cacb604feece489b01bca80e *inst/extdata/dayhoff-dcmut.dat
f6839f30ef8ef1951d6f8c31ca554aa4 *inst/extdata/dayhoff.dat
1775c0260e3cb074806ddb2efd43f722 *inst/extdata/g1974a.dat
25cfbfc89bb17cb4b11d9ad902962367 *inst/extdata/g1974c.dat
84f71769d073c634b23869d10be36534 *inst/extdata/g1974p.dat
663ce2a197685e82374d374549422fa7 *inst/extdata/g1974v.dat
78ff27229ae03ae96d68b2ae04eedb2e *inst/extdata/grantham.dat
6ce233af412c46f1537047c71282f259 *inst/extdata/jones-dcmut.dat
36dbd188f4c29978cd0f645bb5649aad *inst/extdata/jones.dat
33db3a355aa42e9afdefe3f4c75dfe83 *inst/extdata/lg.dat
7647f495e3dd3fd9b37e8cf502f06886 *inst/extdata/miyata.dat
362c479f53105f09d47e4ffbf86c3c8f *inst/extdata/mtArt.dat
7a370a4e2b1589ddd216ecae1f0a4d06 *inst/extdata/mtREV24.dat
c9a8fcb1cff8e17dd4dbc4545c748395 *inst/extdata/mtmam.dat
7e69e80b65ab577e94dd58984a4e5e28 *inst/extdata/wag.dat
b68a39db182ff717aa10b54005fb2c58 *man/000==.Alphabet.Rd
7a349aee72aa20dcc0277b98fee9ab78 *man/000==.Process.Rd
9badb8e59675c56492f2f109124ef12c *man/Alphabet.Rd
1595472cfd6a8b41721287df24b75c5e *man/AminoAcidAlphabet.Rd
d494d380bbe04f3795f2a9c8577a7cd4 *man/AminoAcidSequence.Rd
cbc05f41b196288695bb6c252ba0cb17 *man/AminoAcidSubst.Rd
675cd17f1928c8b09af0fb717291e2a4 *man/AnyAlphabet.Rd
ad093673b8ad463692984c95868689a7 *man/BinaryAlphabet.Rd
c1a179a11b230c61c263111215d7b0d8 *man/BinarySequence.Rd
3de784f6720840f7310eb22f296c0f20 *man/BinarySubst.Rd
043a27f6268db69a5a6594deda8e5f81 *man/BrownianInsertor.Rd
4656b6552070e9c39a26d317d123190f *man/BrownianPath.BrownianInsertor.Rd
0444e5a0088d0c010513f1d8169fe77c *man/CodonAlphabet.Rd
4fdd02cf8676899942afd227b3977976 *man/CodonSequence.Rd
b1fab8dc413b0d225f9d65987bd397f5 *man/CodonSubst.Rd
a8712cc012b55e77c8e09e5364c6b42f *man/CodonUNREST.Rd
311e751a3075b088d33b057df4045ab7 *man/ContinuousDeletor.Rd
56d766baf712aca7a9e8f8b28a352b5a *man/ContinuousInsertor.Rd
8b254ba65193934600bc400e1fd23e6f *man/Debug.PhyloSim.Rd
caff2ef6b5f2592543de7441104587c2 *man/DiscreteDeletor.Rd
9b6dedc6696098800dc4867f83dc08a6 *man/DiscreteInsertor.Rd
81146644bb765f4f9a59a08cc0937ab1 *man/ECMrest.Rd
56434b4f0043069b6391506d2d07ace3 *man/ECMunrest.Rd
c8f1e6a0f51c2eafde1e99f9952bf1ba *man/Event.Rd
897d4e660ac591219470ef7e64b9ee93 *man/F81.Rd
935767234ab75f05577ffa12972c5f12 *man/F84.Rd
a772931431732ae8bb9874afb4d21398 *man/FastFieldDeletor.Rd
6667ae1ab9d4b4438da36f192752e26c *man/GTR.Rd
64e1d3c25afa79f2d94837b181f020d3 *man/GY94.Rd
afb4c574ee786fe8cd9b04e03253d9da *man/GeneralDeletor.Rd
2bb98d60bebbdace1ac3483861b1aba0 *man/GeneralInDel.Rd
c16973fb9414872b3fe66ff884978b6f *man/GeneralInsertor.Rd
9d565e28d24afcba40f1f4c585449e69 *man/GeneralSubstitution.Rd
d077102330c7d5a5bb89e178e73f5939 *man/HKY.Rd
afe39315d9e8033b2ea0455a284a2a93 *man/JC69.Rd
e2c61d9e6bf939236558e3ae446dd2c4 *man/JTT.Rd
9afb38a6faee901bce223fee54aaa353 *man/JTT.dcmut.Rd
52c8d60d88ef07a47024c8069014f8ac *man/K80.Rd
9030bf33c299814543b18e211cafecb9 *man/K81.Rd
a0a63102d1267f7f9275d1bb66d97cbe *man/LG.Rd
b1fa09cda4dcbf68012004f3e84119a1 *man/Log.PhyloSim.Rd
0437fa663b64f66f5d20f1c3f022f20c *man/MtZoa.Rd
96f2d9f5d39c5ac29141284aeef87458 *man/NucleotideAlphabet.Rd
61be8f02851037fa7c47a1e0287f587e *man/NucleotideSequence.Rd
3a964b59baca883333a03759ace4c02e *man/PAM.Rd
f0448e3db722c5384dfd0519abe23aa5 *man/PAM.dcmut.Rd
5af7729fda33676a1b04b8b8cebe7da4 *man/PSRoot.Rd
abd41748060b4ce487d17d5cf25662c5 *man/PSRootSummary.Rd
74e4dae4423aa4c0906a3fe1c0f6d84a *man/Perform.Event.Rd
871b438f3f367b96a8585dd61cc6ae83 *man/PhyloSim.Rd
31e8b8d2e46223cc8bf90a3d410b3f13 *man/Process.Rd
4a8280ef7a27b6f87decfc3d5f094a32 *man/QMatrix.Rd
e5eba5c209a439da682e29295eb13094 *man/Scale.QMatrix.Rd
4487836e0236ff70b0a05cfcf9f1a25f *man/Sequence.Rd
8d0d4cd14ba498d3c3b13f9256ed668d *man/Simulate.PhyloSim.Rd
889d032e2c0d2d24a29d767cb3ad7da3 *man/Site.Rd
72b1545486db81e18632a4232fa98659 *man/T92.Rd
07c969a3516b8ab0e6c7989848e2a644 *man/TN93.Rd
568e4e24c3578736700da6403a5b4cc1 *man/ToleranceSubstitution.Rd
9432e7c8a57ba543694ac913101a13e5 *man/Translate.CodonSequence.Rd
ea483db49593df7b8674e9085e45dd72 *man/UNREST.Rd
408616b48d7f9f68e43bc7e8bc22a769 *man/Undocumented.PhyloSim.Rd
a8706d11d6cf2b264242ce05dc7e8513 *man/WAG.Rd
5ddcc9864c98994ebd064349bc33d832 *man/areSynonymous.CodonAlphabet.Rd
d92062ddb233c6abe4f0fa4b757d6adc *man/as.character.Alphabet.Rd
0e16c3e9f2f1bf2d07ad852a3f124b92 *man/as.character.Event.Rd
8f0d5d3717e6af01301e167853a3fb0d *man/as.character.GeneralSubstitution.Rd
9784848e9ba495044f16bcee87eca4c1 *man/as.character.PhyloSim.Rd
acbd84f1b1e1c0b25525fe6a803be5a5 *man/as.character.Process.Rd
79e60e34edf187f1d2daf0dcd273a2dc *man/as.character.QMatrix.Rd
43e5e7d04e80b707cee64caacc94d09f *man/as.character.Sequence.Rd
2c9dd59b5a7fd5f7f08dc087ebd1ede6 *man/as.character.Site.Rd
233c0ab787499fcadade55f7ad025583 *man/as.character.ToleranceSubstitution.Rd
6ee40720f533235fd0e74655c5b38eff *man/attachHookToNode.PhyloSim.Rd
b0d20b9d71988d357d0573a0a0b90db7 *man/attachProcess.Sequence.Rd
0d6166256aec2a602d246494ddfeef5d *man/attachProcess.Site.Rd
20d03f748c95534f6efd06778eed3bc0 *man/attachSeqToNode.PhyloSim.Rd
e08bf06891aa9ae90eed6b43e63a7e56 *man/buildFromPAML.AminoAcidSubst.Rd
838e74ee8db1a01888d3e4ee9c5b9681 *man/buildFromPAML.CodonSubst.Rd
eaacf4ebc1c2333d2c16c35b135e07a9 *man/checkConsistency.Alphabet.Rd
4d48cca6ef4ae6f53254b338df397b2a *man/checkConsistency.AminoAcidSubst.Rd
549eef205285586173e4806dbd1c8304 *man/checkConsistency.BinarySubst.Rd
975420f94e2fe2acdf719a7781f4afd0 *man/checkConsistency.BrownianInsertor.Rd
5b90d21f14fd3ef5f7a29218c38eee89 *man/checkConsistency.CodonAlphabet.Rd
68247e47501f5c77259cfd03293ef095 *man/checkConsistency.CodonSequence.Rd
59ced7f2f5c28415e174214a293a2299 *man/checkConsistency.CodonSubst.Rd
078ef63ba7a237a622c83c5115c41148 *man/checkConsistency.CodonUNREST.Rd
a2aa2f5ec6015da45fe46229b1c55953 *man/checkConsistency.ContinuousDeletor.Rd
d86e307e8007c0a548707e845060cb10 *man/checkConsistency.ContinuousInsertor.Rd
a08fb4a3f45700e20991f3fc2635d994 *man/checkConsistency.DiscreteDeletor.Rd
5822a83beb0efb9a90cbb460421a275e *man/checkConsistency.DiscreteInsertor.Rd
dae9cec802f3252d63f12f881a6b6180 *man/checkConsistency.Event.Rd
4dc712b2a7ab789b067d1e2737e6e9a2 *man/checkConsistency.F81.Rd
ed2bda9c7058ec4283672e2d02e372cd *man/checkConsistency.F84.Rd
50e9b84d3f2dad81a45f8928d9feae14 *man/checkConsistency.FastFieldDeletor.Rd
c4d1049a3c86c1888d7614acc335a72b *man/checkConsistency.GTR.Rd
92ec79f541b4bbdeb98a5f00f49c33f2 *man/checkConsistency.GY94.Rd
c45a1ceaf8130c7dfafca0fbfb57854b *man/checkConsistency.GeneralDeletor.Rd
6068f89b4c5cd58e4104c14cb202484a *man/checkConsistency.GeneralInDel.Rd
7fbef4d0b2f1a9419cc1c1901ae47e18 *man/checkConsistency.GeneralInsertor.Rd
1c2f546425a9a55886753a7892d2fa94 *man/checkConsistency.GeneralSubstitution.Rd
cb1bf156131463700664c7797f8a3650 *man/checkConsistency.HKY.Rd
52ebe797f52663cc223e9edba397377d *man/checkConsistency.JC69.Rd
9f94b4e864cf1b8bd19aeb64183775bb *man/checkConsistency.K80.Rd
0514df3c35853319a451b46d308cc237 *man/checkConsistency.K81.Rd
0a1d55dd8c988feb1e1f2c193bb2bf12 *man/checkConsistency.PSRoot.Rd
c53d2b1c63c2cdfd2a165c87b76492a4 *man/checkConsistency.PSRootSummary.Rd
e744a24642f754e502d8daffde42dc92 *man/checkConsistency.PhyloSim.Rd
f386a95e45b661135b7ea700b5aa6c54 *man/checkConsistency.Process.Rd
ee0b80987c2254d6b895f8c6812e7907 *man/checkConsistency.QMatrix.Rd
ff59c37a76f87ee95ae6d4d08c4be467 *man/checkConsistency.Sequence.Rd
98d14fa4b2286abb11bfec156b6f14a6 *man/checkConsistency.Site.Rd
56446075b0644a811cd4cc856f5c5048 *man/checkConsistency.T92.Rd
93af9b029039db2b5d80237becf510b0 *man/checkConsistency.TN93.Rd
23811bfef9c993a8d31d32e12e793976 *man/checkConsistency.ToleranceSubstitution.Rd
e5ca77486f8c3dd6f14096a26cffdd1f *man/checkConsistency.UNREST.Rd
353b034bcc4d4b7c7a2acdcbafef1f7d *man/clearStates.Sequence.Rd
7ea887981f7fc6011a3c01130e4b89eb *man/clone.GeneralSubstitution.Rd
c0e0bf762f83994ead2cc6306da9dabf *man/clone.Process.Rd
bc4fde3e0bc6a0c1a8535ca92d97fc29 *man/clone.Sequence.Rd
37908b53e781488fd1700a49a55bcf54 *man/clone.ToleranceSubstitution.Rd
5573b5e7f47e165046d280a488b69a10 *man/copySubSequence.Sequence.Rd
f36bbce64d26d95f3525cee1194a8367 *man/cpREV.Rd
413dc72d72256b86f6b5f8afab81f8bb *man/deleteSubSequence.Sequence.Rd
ec634445f606c52e0cecb191eb456135 *man/detachHookFromNode.PhyloSim.Rd
9ae6744862241a11b5a9273eca4ad81d *man/detachProcess.Sequence.Rd
45ec7301383f6a1b2046dff6b0d5389c *man/detachProcess.Site.Rd
ec5157ad5527ada633831a18116e1f41 *man/detachSeqFromNode.PhyloSim.Rd
28809543f22b5de892b518b473d2702e *man/enableVirtual.PSRoot.Rd
ea5a32213696a27d192fd0b3790d9dee *man/exportStatTree.PhyloSim.Rd
c729463f8a4914b9f567a8f3f8144be4 *man/flagTotalRate.Site.Rd
c1c219355060aad9b0c9ab1cd40d85ca *man/generateInsert.GeneralInsertor.Rd
63e02de1f8998f5f80dc37d0fb23c06b *man/getAcceptBy.GeneralInDel.Rd
d8e741bfea424d126337c19b0524a63f *man/getAcceptWin.GeneralInsertor.Rd
a3200faab7b83694fea8b3d2c0807434 *man/getAlignment.PhyloSim.Rd
1560ec23ffbd962dc5956401add774b3 *man/getAlignmentLength.PhyloSim.Rd
dab5e6e21aacbf6b53bd7c4692fa9aeb *man/getAlphabet.GeneralSubstitution.Rd
de176502bacc94c8bb6e7d424e9f328d *man/getAlphabet.Process.Rd
27c70e90a30e5c59316d930d7e42f308 *man/getAlphabet.QMatrix.Rd
93458975b66a529771f38cf829fa8689 *man/getAlphabet.Site.Rd
2d5b03d95cdfe1fb1a9c0630142543cc *man/getAlphabet.ToleranceSubstitution.Rd
40b1bbd2466145682e7369e931ebe40c *man/getAlphabets.Sequence.Rd
a4c095ea75d9442cc8e93fa8e1edab9c *man/getAncestral.Sequence.Rd
8ff89cffe2c98185d602d6eae8259075 *man/getAncestral.Site.Rd
a20e5b022725b3a4bc3ec6d344807a11 *man/getBaseFreqs.F81.Rd
f7f82e4f778b7176243fbd228827fcf1 *man/getBaseFreqs.F84.Rd
4113975b6f7c339a8e0f99e92307de7d *man/getBaseFreqs.GTR.Rd
d75b5980e9d7abdc10ad05e1f290b790 *man/getBaseFreqs.HKY.Rd
0b8fdae1e23ceda3333cb67e8e9763c2 *man/getBaseFreqs.K80.Rd
7821ba040ce3566e0c8ef9317569eb8f *man/getBaseFreqs.K81.Rd
ef80655c4625ac5c4684ddbbd72af72e *man/getBaseFreqs.TN93.Rd
7facc392d23b9e091268269d20fbcf06 *man/getBigRate.Sequence.Rd
a7abea573edb386b28fe4fd3fd8cb5a0 *man/getBranchEvents.PhyloSim.Rd
d578c674020d93d4d2bca01d8be59b63 *man/getCodonFreqs.GY94.Rd
9847e090ce9346d96de7a7dc2dd10892 *man/getComments.PSRoot.Rd
610f316d8f1204a88cee38ae9bd8b91a *man/getCumulativeRates.Sequence.Rd
71b6f702e23f674f29bda6751606d4b8 *man/getCumulativeRatesFromRange.Sequence.Rd
9971f8d9018d0ef3ed4d2203c33a96cf *man/getDeletionTolerance.Sequence.Rd
709b263e9a03b9053ad8840b9aa4c7a6 *man/getDist.ContinuousDeletor.Rd
4e367120814ceef749a289d2aeb21420 *man/getDist.ContinuousInsertor.Rd
d0a42bbf96e2d8b45ec1f79b01f3839b *man/getEdge.PhyloSim.Rd
c34fea6e2e7d4e31494a9a10ffc0aca0 *man/getEdges.PhyloSim.Rd
8455318ed262049152e20b6a9937c64b *man/getEquDist.GeneralSubstitution.Rd
4257dd5b2b3f251cc7e5e052aecd36e9 *man/getEquDist.ToleranceSubstitution.Rd
8c6f50ed748ff0e36141785f2bd4b953 *man/getEventRate.GeneralSubstitution.Rd
953cd5c175c75e6de6e47b812e95f2f2 *man/getEventRate.QMatrix.Rd
482870cd188322a94a71f32736f0821a *man/getEventRate.ToleranceSubstitution.Rd
2da35f38d211864a9e95d892f1f705b8 *man/getEventRateAtSite.GeneralSubstitution.Rd
818089c16ba29ba13a3d6ccd173906cd *man/getEventRateAtSite.ToleranceSubstitution.Rd
666dba789a17fd81d642868b063990e8 *man/getEvents.Sequence.Rd
c639cc3ebf135ed204d6d129908e6feb *man/getEvents.Site.Rd
17622748dd01ee65665b062f15a35e10 *man/getEventsAtSite.FastFieldDeletor.Rd
a4fe582a8967638a54fcc08fa91741d9 *man/getEventsAtSite.GY94.Rd
730df3114ca4e872667e4a6cf986bfb8 *man/getEventsAtSite.GeneralDeletor.Rd
8b141d60570a235499ead02f4b13dfd3 *man/getEventsAtSite.GeneralInsertor.Rd
38dcb1f11612365347e2ca46d205e44c *man/getEventsAtSite.GeneralSubstitution.Rd
09b24e52bc6154f5ae27264ae3d95f81 *man/getEventsAtSite.Process.Rd
7ede919be6fce5d2f3149f7cc5d81d52 *man/getEventsAtSite.ToleranceSubstitution.Rd
40663bf51911d4ab78f8cc92eb211ae8 *man/getGenerateBy.GeneralInsertor.Rd
ef754fb47ad7e95216911fb93d970b81 *man/getHandler.Event.Rd
f754b8136f6487222e63d24ec00c6136 *man/getId.PhyloSim.Rd
d321bafc50a3fa59a26638a56ed0b012 *man/getId.Process.Rd
98250938e3780f86f78c3db9fa20f9e9 *man/getId.QMatrix.Rd
ec4a7c94a72695398a8a2b81822dfef6 *man/getId.Sequence.Rd
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3a8cdd4002f1ebedb04b1dcebf9c0d7b *man/summary.HKY.Rd
0b95226e3df644d981e7d00876228f92 *man/summary.JC69.Rd
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3e285d55350a9162fa9e439ca78caa12 *man/summary.K81.Rd
7e8b7613447bc699dfd342fbf446f184 *man/summary.PSRoot.Rd
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2c5c5ebe042b01cd39513b9513bb31dc *man/summary.ToleranceSubstitution.Rd
503c91ddafd6b738219337f73a313aed *man/summary.UNREST.Rd
3b72c6ec42147e8f6424c5ade9d436a8 *man/translateCodon.CodonAlphabet.Rd
7d359ce27559bba97323b330bcc7b427 *man/virtualAssignmentForbidden.PSRoot.Rd
bf371449807ac728171c01ab4fbe0306 *vignettes/Makefile
1d3e687aec2e6c74f84ddc3dd9af7931 *vignettes/PhyloSim.Rnw
