378baf354e64e6b91c9ca3a1b3f8c08e *DESCRIPTION
06ffa58d2e572f7dda8585c17a98ac63 *NAMESPACE
7a2ccffedc323ad9f02d0058fad013f7 *R/Alphabet.R
13d32c17283616ebfc6ed0ae0ff30201 *R/AminoAcidMatrices.R
c8ce3754268b939a6830830547010309 *R/AminoAcidSubst.R
c187a9bde2ef3ab4eadc8c4a304af0fa *R/BinarySubst.R
652347048cfdbbb71074e00555530cbf *R/BrownianInsertor.R
333a726d0e2f4f0eacbd9066dac1a6f4 *R/CodonAlphabet.R
a111e10ab32c1aa53a80a6e2d5298aa1 *R/CodonModels.R
8657b4e727b44b1a6beb7c81fb687ca1 *R/ContinuousDeletor.R
2c247b42b7024a70da622cdfdd709049 *R/ContinuousInsertor.R
d6994f94aea6d6b6ab04641e545b1e48 *R/DiscreteDeletor.R
bb26d26ef684625cabef84122a414c67 *R/DiscreteInsertor.R
ce4ac1945618478e7c4525ea53c19c68 *R/Event.R
9d215524e2f8e0a6e0488f6c27ff413f *R/FieldDeletor.R
a23736811e89e9bdda791d2d2ec6c5dc *R/GeneralInDel.R
561590efb379d099f620ae35456d05af *R/GeneralSubstitution.R
021242e504c156c6e77dc4e5c855dab5 *R/NucleotideModels.R
7e97fdd11f1160a8451c0e4031fbb521 *R/PSRoot.R
60f6cf5fe8e3fb75e30c8f02c54d728c *R/PhyloSim.R
144127d310cf980c01ffefb1030042d4 *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
76a2af4bc4dbae1922c4d4303571b334 *data/JTT.RData
24d7bfa7cebe4eb9a231ac989f9c7e01 *data/JTT.dcmut.RData
07fbfa42042a045cdae3d6c650d9ac83 *data/LG.RData
94f5149b03df065a000769a2a9b3af7c *data/MtZoa.RData
59b641c7b3589a51907841e2bb31f334 *data/PAM.RData
0b65b4857d2a7226ce09fe2c207e6e6b *data/PAM.dcmut.RData
09a531d330f2467886ac56274f849be3 *data/WAG.RData
1c7b014c935c4de0d6f3312c0c8b905a *data/cpREV.RData
cbad00204c8aad4d43175c0f5e30b92b *data/mtArt.RData
0acdbedd1d092d976f1fec3402d011b3 *data/mtMam.RData
c5c679949de7f2932bfbda4d4d4ee92d *data/mtREV24.RData
c0582b4193e3d35d748d8f6d90b305cf *extdata/MtZoa.dat
61a899bae16d1eeba9a77b5f8a7a1783 *extdata/cpREV.dat
f1326e01cacb604feece489b01bca80e *extdata/dayhoff-dcmut.dat
f6839f30ef8ef1951d6f8c31ca554aa4 *extdata/dayhoff.dat
1775c0260e3cb074806ddb2efd43f722 *extdata/g1974a.dat
25cfbfc89bb17cb4b11d9ad902962367 *extdata/g1974c.dat
84f71769d073c634b23869d10be36534 *extdata/g1974p.dat
663ce2a197685e82374d374549422fa7 *extdata/g1974v.dat
78ff27229ae03ae96d68b2ae04eedb2e *extdata/grantham.dat
6ce233af412c46f1537047c71282f259 *extdata/jones-dcmut.dat
36dbd188f4c29978cd0f645bb5649aad *extdata/jones.dat
33db3a355aa42e9afdefe3f4c75dfe83 *extdata/lg.dat
7647f495e3dd3fd9b37e8cf502f06886 *extdata/miyata.dat
362c479f53105f09d47e4ffbf86c3c8f *extdata/mtArt.dat
7a370a4e2b1589ddd216ecae1f0a4d06 *extdata/mtREV24.dat
c9a8fcb1cff8e17dd4dbc4545c748395 *extdata/mtmam.dat
7e69e80b65ab577e94dd58984a4e5e28 *extdata/wag.dat
8684a6b77561352afcf31fb104a62988 *inst/doc/PhyloSim.R
1d3e687aec2e6c74f84ddc3dd9af7931 *inst/doc/PhyloSim.Rnw
0bf11486e0c1b07c2b319a5454d704e5 *inst/doc/PhyloSim.pdf
fe48cc93143e5404336df5c1595ed0a8 *man/000==.Alphabet.Rd
ecd3ba2b555b0400c7a1c64093d763bf *man/000==.Process.Rd
9e0cedf6404129491152c82f2a15fee5 *man/Alphabet.Rd
2b7fc39c281cc1e8d3dab223ff3df02d *man/AminoAcidAlphabet.Rd
50f02b797d8bc4ee68b794770dd4402b *man/AminoAcidSequence.Rd
ecb513a3a7a583d2cfba522e9d7bc6dd *man/AminoAcidSubst.Rd
0ef0ef933947a503986236877f8dd75f *man/AnyAlphabet.Rd
ac2f6483929ba7f3784b991135bc0dd3 *man/BinaryAlphabet.Rd
204fece98452898f8161b24c626ea18c *man/BinarySequence.Rd
fe8135fd03763353f23b780e7ecae184 *man/BinarySubst.Rd
4c9251019f72937d8133179760fd1fe7 *man/BrownianInsertor.Rd
e139e5a7c201f8e83b383bc2890e129c *man/BrownianPath.BrownianInsertor.Rd
be1be97a0d5dcf74e6a83027b530fbbd *man/CodonAlphabet.Rd
6f2d1bfc5b9f29c2949a12e5403d2052 *man/CodonSequence.Rd
32e791ceba30be3d37fa2b2d03b79b2d *man/CodonUNREST.Rd
63f616e7f88be810f143e0706c80606c *man/ContinuousDeletor.Rd
273eb2bc2f94cb54243d6462c07628b3 *man/ContinuousInsertor.Rd
3fc510f989543ed8520d95d8c8f529d9 *man/Debug.PhyloSim.Rd
f3041789c617f498b244a416c7e7c136 *man/DiscreteDeletor.Rd
c5c3a706fd72aff562c50bea44307c81 *man/DiscreteInsertor.Rd
2b9643295ac067ebd02d68b1640709e5 *man/Event.Rd
826912ee82f0a57f615ca01f97807848 *man/F81.Rd
8ba2c2ff1077b9196786ce83114206ae *man/F84.Rd
fa45af9737533d01fb98f26c66a1626e *man/FastFieldDeletor.Rd
f910b37e069007401151f625f4c0ad71 *man/GTR.Rd
e02e5e77949d639e36234b83aca85d16 *man/GY94.Rd
e7a7c14ef88a16fc42a565047bd19a32 *man/GeneralDeletor.Rd
a4cf1f40282cd033c676f5aa031597ba *man/GeneralInDel.Rd
2175e9e6a082c5f885593b5effc3a93f *man/GeneralInsertor.Rd
d2a58224a1b20a7ea500b313e160d708 *man/GeneralSubstitution.Rd
5fde56c8899f77ab87ef1bab36c606ad *man/HKY.Rd
f72eb5c8bb902fe2df937cf41d3833b3 *man/JC69.Rd
567daf9e0b7be5458c3cc966b6502e36 *man/JTT.Rd
ab3c5a36b50f5540fe829df4b069b6f0 *man/JTT.dcmut.Rd
03df7eec2d083daa490e93a5c67be53b *man/K80.Rd
9b45cbb7efc2409929175e0efc1ff561 *man/K81.Rd
1747e0e96c75c406101b1b53a9977a96 *man/LG.Rd
ba337f22912391f0a201a71e60511f92 *man/Log.PhyloSim.Rd
15028ec66ca4628fd01a950d228868b8 *man/MtZoa.Rd
212059378feb36668f2bd47f8d80dc34 *man/NucleotideAlphabet.Rd
0e9a841f237e10440f0af50757615b5e *man/NucleotideSequence.Rd
89c5a12f6930630f4f56aea21d5d0090 *man/PAM.Rd
461e40fc9007326dae9c9b6aba94248c *man/PAM.dcmut.Rd
0ee6e39297f8589458401a91caa2fa51 *man/PSRoot.Rd
3ddfdad0812873a2e84b9ee7e5921a40 *man/PSRootSummary.Rd
046091eb6d9db8fee60e3731e48ff396 *man/Perform.Event.Rd
ad6da01faf9557e4474520122a66c922 *man/PhyloSim.Rd
35ed59d97ed560bbbb94bc6c3ec290e2 *man/Process.Rd
2ab71e6da5a61e8d5e55fe1f279c422c *man/QMatrix.Rd
e3b39e1ada2733022cb82c6f7f475fb9 *man/Scale.QMatrix.Rd
c96262d2778a84bc5359a8413d64c4a2 *man/Sequence.Rd
43ec71453daa5c4e5e7da44b81576841 *man/Simulate.PhyloSim.Rd
ebb6db41bcbbae45f1f039b6b4f04237 *man/Site.Rd
036f31cea6cf75aedc9a3ce91c23c4c8 *man/T92.Rd
eed4108c540d23e82f2e0758f450fd48 *man/TN93.Rd
9decf130f2309da5e8f4204376c4f2f7 *man/Translate.CodonSequence.Rd
86c2142dc0a81334a6c7198687a78a79 *man/UNREST.Rd
2a562a66707a1d90d63d1d82e3f81ecb *man/Undocumented.PhyloSim.Rd
4fd721c5a249aba11e0a715fe6d3b395 *man/WAG.Rd
c72d67249a57c6a8c6cacae497d0c8f7 *man/areSynonymous.CodonAlphabet.Rd
b72f72bd406e2707a152e3cc9a592f49 *man/as.character.Alphabet.Rd
f3adebee7a8fec0a759217b04b5ac6b8 *man/as.character.Event.Rd
8a0e0d5befb3f8c3de9467fa85caa7a1 *man/as.character.GeneralSubstitution.Rd
697b92bc64c8bcf292a86e70af4c3a57 *man/as.character.PhyloSim.Rd
1f8cf67a38c520e47031a14da01edcaa *man/as.character.Process.Rd
cd0d6b3daeb8328ff78eaacd83c8b16f *man/as.character.QMatrix.Rd
f8915169aa661b19a87b2bda768afef3 *man/as.character.Sequence.Rd
e105f8d3eaf9acda8fc772ba207e2ef1 *man/as.character.Site.Rd
17d81cd5713db2ced95b52b65ee9d466 *man/attachHookToNode.PhyloSim.Rd
42a311f19183670c4ce08f1c83b4aeca *man/attachProcess.Sequence.Rd
692cf7926f0aa68c7264af40536a4a74 *man/attachProcess.Site.Rd
ed344299c501fc0ee4036dd67eac18c0 *man/attachSeqToNode.PhyloSim.Rd
f4b2f94d464a8cdd149a58e27bb29b0b *man/buildFromPAML.AminoAcidSubst.Rd
ac455dbbe3eb02206658b334c2c13edb *man/checkConsistency.Alphabet.Rd
2fd2041aefc96926296d9ad6e4f0d790 *man/checkConsistency.AminoAcidSubst.Rd
bd8917d60e29a6c5388487704ffaec19 *man/checkConsistency.BinarySubst.Rd
ff11ebb262829187cc92dca63b92e255 *man/checkConsistency.BrownianInsertor.Rd
e615aa028a853dae69266522aeb911fc *man/checkConsistency.CodonAlphabet.Rd
5253c1f60df4e98dda3f71d792b8fe29 *man/checkConsistency.CodonSequence.Rd
b8fc259bca6ccf66712ef79d3977372a *man/checkConsistency.CodonUNREST.Rd
c799016e468a347c729b20466ea25564 *man/checkConsistency.ContinuousDeletor.Rd
fc8a57cabe72e66e5bc4be0d009d7852 *man/checkConsistency.ContinuousInsertor.Rd
8352d38e1d43865a3e8edce73850b352 *man/checkConsistency.DiscreteDeletor.Rd
f37f1fdfb4088fac2943e7a9f7d0af27 *man/checkConsistency.DiscreteInsertor.Rd
b70460c705190a09e637ebd8b65af004 *man/checkConsistency.Event.Rd
9abbfda39a277564eb0dbfc1596968e9 *man/checkConsistency.F81.Rd
3c1df557962794e83dc1e2b477419757 *man/checkConsistency.F84.Rd
d194b94ddb3842617807b876fa373003 *man/checkConsistency.FastFieldDeletor.Rd
9a2dfc3ac0b0a5c97aa47790383276f5 *man/checkConsistency.GTR.Rd
51db6bd4a4d46490ada47122273e5312 *man/checkConsistency.GY94.Rd
e4de6ff9afbc1082c30af549509a232a *man/checkConsistency.GeneralDeletor.Rd
d7fac69998c1064eade67dcfe1e7c645 *man/checkConsistency.GeneralInDel.Rd
480c5cc96b314f96f33d683b067d2aa9 *man/checkConsistency.GeneralInsertor.Rd
629a6268d769ce3fa9086aad9271cfb9 *man/checkConsistency.GeneralSubstitution.Rd
fff958b33b6cd1e7773828326de74f08 *man/checkConsistency.HKY.Rd
09132f0c907776ac304861ef2f19a107 *man/checkConsistency.JC69.Rd
67df4723d24718937676dde79ccb8aec *man/checkConsistency.K80.Rd
5a45803a4df72f9985278e19b51fb257 *man/checkConsistency.K81.Rd
92cc66b00fb4937122cb8d5e6ccc56cd *man/checkConsistency.PSRoot.Rd
f8b59fa9203523d019b70bc52465139b *man/checkConsistency.PSRootSummary.Rd
fe8baf09484efc2b9f876854e2b27d59 *man/checkConsistency.PhyloSim.Rd
32097cf3b7ce2b1fc175d4b2f811fedd *man/checkConsistency.Process.Rd
e324eea6c6be4136fcde879cc6c2eccc *man/checkConsistency.QMatrix.Rd
bc0d901048078ead6169151f124b2bac *man/checkConsistency.Sequence.Rd
79024d32008a522b142810fad2099a5a *man/checkConsistency.Site.Rd
b806225109657d6a2e1add3851f14d43 *man/checkConsistency.T92.Rd
5197170b28b27659956aed05141854c8 *man/checkConsistency.TN93.Rd
6efaba724e008befec4d7a2900849430 *man/checkConsistency.UNREST.Rd
e383f4c5f77d5c948535de5a7252ce71 *man/clearStates.Sequence.Rd
8778092781d1707f591305b3fce34b21 *man/clone.GeneralSubstitution.Rd
521b1c4561a07798f951dff32cf5fe9a *man/clone.Process.Rd
86e12294794f9dcd373b2104d7a04f4f *man/clone.Sequence.Rd
ca641cf77cdfdef02265aeb7f1613c62 *man/copySubSequence.Sequence.Rd
7e798f93a76d52f8e7982908ab9110b8 *man/cpREV.Rd
964639c982cf3283223b83b56b1ca564 *man/deleteSubSequence.Sequence.Rd
c4fd3c2c8d7587241ac68c6cb4d99734 *man/detachHookFromNode.PhyloSim.Rd
0517c40506588d58b1015bda2e3886b3 *man/detachProcess.Sequence.Rd
0f6c477dd1901612193d411c2ad1fb9b *man/detachProcess.Site.Rd
1a69b3aa99d214ada6cead02360b68c5 *man/detachSeqFromNode.PhyloSim.Rd
20bf30e3995e62830fb8a13604ef469a *man/enableVirtual.PSRoot.Rd
e33abce3def53fa412a393d70f434c8e *man/exportStatTree.PhyloSim.Rd
e1d5fd38c373bb9fb8534a589282ab94 *man/flagTotalRate.Site.Rd
6707a22431abd65c8f40bec19a2ff1f0 *man/generateInsert.GeneralInsertor.Rd
da780155f6a640f923fbe2b2d362d2a0 *man/getAcceptBy.GeneralInDel.Rd
365ce1711b7d9c81b17dfbd28794c0c7 *man/getAcceptWin.GeneralInsertor.Rd
a13b894bbbd7103fd184058d6e129428 *man/getAlignment.PhyloSim.Rd
4489971457262081b59eafd5dfcd374e *man/getAlignmentLength.PhyloSim.Rd
f55ddce98369167f0be9bf68146b69d9 *man/getAlphabet.GeneralSubstitution.Rd
9b31d280cc0e0f2ce46ab939b73e30c0 *man/getAlphabet.Process.Rd
ddf77dbcaa510c1ee1a2a3053188ee10 *man/getAlphabet.QMatrix.Rd
0e26bc2aa86ad1f2b5993c26c6041299 *man/getAlphabet.Site.Rd
20fe2208709e0f08f814490d2436dfd1 *man/getAlphabets.Sequence.Rd
76e85d827d9b1fb3a79694bd83fb305f *man/getAncestral.Sequence.Rd
c140b188ca70e5d542d509e7c7a42508 *man/getAncestral.Site.Rd
29b6f73a3884cf888e47539d24638300 *man/getBaseFreqs.F81.Rd
4d4ba2a23db28d07623c4039e4592f71 *man/getBaseFreqs.F84.Rd
f86b4ddad63015185661fda48cce7a61 *man/getBaseFreqs.GTR.Rd
88719a1070fae331d8e2bff114b0a739 *man/getBaseFreqs.HKY.Rd
1bb0125cf839032eb6adacbcfca7ceff *man/getBaseFreqs.K80.Rd
850e22a351510dda979d17d4e8a6b445 *man/getBaseFreqs.K81.Rd
bf9eab910ee2a0998061a8e2a09146cc *man/getBaseFreqs.TN93.Rd
a7f484d95039c42e2424df187a4f6b1c *man/getBigRate.Sequence.Rd
9739e1510fc721b9d70acf25b7ffc1ac *man/getBranchEvents.PhyloSim.Rd
5f22071e019b66c5e1fdc55add681f6b *man/getCodonFreqs.GY94.Rd
3f9409d8b349ea872f345afac875e113 *man/getComments.PSRoot.Rd
d327ce6dc06dc1f68b44f3a0bdbf81a8 *man/getCumulativeRates.Sequence.Rd
a6dbb622406981ea0599f797b5f87b92 *man/getCumulativeRatesFromRange.Sequence.Rd
e1a105092a3ada97a447bfa43c129835 *man/getDeletionTolerance.Sequence.Rd
7ec6d7aecd3a7516f3b4f80330fdec32 *man/getDist.ContinuousDeletor.Rd
295901149a4304ae1e8f5e8fa6bc8a6c *man/getDist.ContinuousInsertor.Rd
762f75d6b9cb08dcbe1e39877d38b17e *man/getEdge.PhyloSim.Rd
52071ea01c8c37f7fbd9778da746bccf *man/getEdges.PhyloSim.Rd
e081c1d8d933845142bf65304e2819cd *man/getEquDist.GeneralSubstitution.Rd
9e6313806e922cd71783863c95eed69d *man/getEventRate.GeneralSubstitution.Rd
ded691bfe470495cadb8eb8009430f5c *man/getEventRate.QMatrix.Rd
edef4972ca4a593fbe4ce18ae1e78156 *man/getEventRateAtSite.GeneralSubstitution.Rd
ce6936cbfc4d74059166d2bd97508459 *man/getEvents.Sequence.Rd
8a970b7f5988ff8bc8c2344d48e64eea *man/getEvents.Site.Rd
fdae24fb4dce18cdff294faf538729b6 *man/getEventsAtSite.FastFieldDeletor.Rd
2c4b19ab6b816ed8612cbf7153a53d50 *man/getEventsAtSite.GY94.Rd
7c838d0d036fa892c52205023f0c4d96 *man/getEventsAtSite.GeneralDeletor.Rd
62251b93206f61eb8625efa436d94e51 *man/getEventsAtSite.GeneralInsertor.Rd
d851dbfadf39a1c69d2b651b8cddd270 *man/getEventsAtSite.GeneralSubstitution.Rd
a1a2968d6e29fdad910699a2a9667c28 *man/getEventsAtSite.Process.Rd
37284220a16bc5012ba62eebbc1bb537 *man/getGenerateBy.GeneralInsertor.Rd
dd4e8cc1d2e2c36447df10835f18181a *man/getHandler.Event.Rd
10c45d8d31808cb0d42e1ea41d5b155f *man/getId.PhyloSim.Rd
3acc9f18976575a1d0ffcaf6a797ed1a *man/getId.Process.Rd
bf292f3b41df824a189bec1bc39032c8 *man/getId.QMatrix.Rd
39710b29a36af58f9fcd3022d7dadc00 *man/getId.Sequence.Rd
88cdebe3fefd8fa78d7c8de7c7a13abf *man/getInsertHook.GeneralInsertor.Rd
b57e98c29d834f3f81fcd53ef0dbfd29 *man/getInsertionTolerance.Sequence.Rd
fe3b77b53cf035639fd8ec5bfb020530 *man/getKappa.F84.Rd
27068b9ab222a9cff9bc0c8bbd057146 *man/getKappa.GY94.Rd
f21a9aacaa27457490e92488c814b966 *man/getLength.Sequence.Rd
41dca7ce164192717abff5343f08d045 *man/getLengthParam1.FastFieldDeletor.Rd
4772afa9a82cfcc2b6658b44cf17553e *man/getLengthParam2.FastFieldDeletor.Rd
f5a95e05e69f1ffa5c9d8be6a6d4b313 *man/getLogFile.PhyloSim.Rd
51002a24ab4209c15315fa3a6035392f *man/getLogLevel.PhyloSim.Rd
d78e4cd154d883b461352c7483539ecc *man/getMatrix.QMatrix.Rd
3b62c663b1b14ed9a7e4848192d68857 *man/getMaxLength.ContinuousDeletor.Rd
eac12578fd54bd832f20e4c91376607a *man/getMaxLength.ContinuousInsertor.Rd
b84e78234caa359d7cb7713dec5146c1 *man/getMethodsList.PSRoot.Rd
ee25d89bc966aa14b8e18de092764258 *man/getName.Event.Rd
059facdcb7c8f8f10faae5c7a7b3e34a *man/getName.PhyloSim.Rd
3b7557e9e0aafad0acf1f49d6eb26702 *man/getName.Process.Rd
e0e6642019ce76664f8234202f2ebbc9 *man/getName.QMatrix.Rd
d6b8f1a6f7e91fdfaf658c6156d60cc7 *man/getName.Sequence.Rd
732799f11b5f7aa0728cf1e5f9a1fb52 *man/getNedges.PhyloSim.Rd
28e5c727e43a105b31515c6fbf6bb6bd *man/getNodes.PhyloSim.Rd
deb7e139e023ef6147d92d69cd32594b *man/getNtips.PhyloSim.Rd
85748f30cb476b3b9c5af74864987490 *man/getOmegaScalingFactor.GY94.Rd
2f467fa1765feabe27f552b5d594816e *man/getOmegas.CodonSequence.Rd
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2fc28366871a4994e28827ee6770dd84 *man/setSizes.DiscreteInsertor.Rd
19724c495c0f23a8186b074910f7e8a9 *man/setState.Site.Rd
d699439482ce9c0f69ebfad330fa022d *man/setStates.Sequence.Rd
c4602d88115061b77470ccf7cf200384 *man/setString.Sequence.Rd
368ff79056f5a485fad17b219a0629d4 *man/setSymbolLength.Alphabet.Rd
2843f5745750c7799876e1707379a0b7 *man/setSymbols.Alphabet.Rd
498f1f04550bd7e63d68e09a53eb45a6 *man/setTableId.CodonAlphabet.Rd
301c28cc0494015b9ffdb445bb37e170 *man/setTemplateSeq.GeneralInsertor.Rd
199fdc7d6cb9947f5ff4c584488cf2bf *man/setTheta.T92.Rd
e84b46d758493db71af3ad22533753a2 *man/setTipLabels.PhyloSim.Rd
ae91cb29aa2b57302e2e5483f15859d0 *man/setTips.PhyloSim.Rd
0a877113eff1f623f199d0732c02fb02 *man/setToleranceMargin.FastFieldDeletor.Rd
03b980fdc3d98bc8b7d07516d39aeeb2 *man/setTotalRate.Site.Rd
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3249c6ef3826e7ffc1464b3f05bb8abb *man/setTransTable.CodonAlphabet.Rd
28ecb0ca524360e95edbb17dc07c073a *man/setTreeLength.PhyloSim.Rd
1efdbd766adb2cc45f2eb0b39c8d275a *man/setType.Alphabet.Rd
246a4fac127b9f43e12fdfa59f2bc970 *man/setType.BrownianInsertor.Rd
84f9e52d9a098fa2cb54dab23b0c6c70 *man/setType.FastFieldDeletor.Rd
2da0114de684593b482fb6f5a0b18b85 *man/setUniqueAlphabets.Sequence.Rd
3d7d7e969dc7d54d1dbd21c0615cf4c5 *man/setUniqueProcesses.Sequence.Rd
7402b65e05c807e39347e679a47aa8a3 *man/setWriteProtected.Alphabet.Rd
152f0d4481ef5a379be04594978a9168 *man/setWriteProtected.Event.Rd
2f4efce147aa80c349d41fabf8635ed0 *man/setWriteProtected.Process.Rd
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5dc464829db50523a1014ea61a77470c *man/setWriteProtected.Sequence.Rd
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92d6b6a82b13c3af580e47195436211e *man/stringLengthVector.Rd
911dc40f67a80f324dc6422ff4514038 *man/summary.Alphabet.Rd
ccb1ee1edaa98f1fd2a6182e7c05d48d *man/summary.AminoAcidSubst.Rd
dfbd1b4d3e3e7b83955c1c1a6460e87a *man/summary.BinarySubst.Rd
f1400c8574e18cf66d4851d68104d088 *man/summary.BrownianInsertor.Rd
fb46d2b0032a4728b937b125a1df308a *man/summary.CodonAlphabet.Rd
f654d57b9da930cd433218e8f5f8b4ff *man/summary.ContinuousDeletor.Rd
9f93163daa6cf5a650e80019207c0b14 *man/summary.ContinuousInsertor.Rd
733430e9162d10cf62c8487f6f010512 *man/summary.DiscreteDeletor.Rd
28699ea991936324d2272ce064cc1d36 *man/summary.DiscreteInsertor.Rd
fb0fa0a95480a9c689aae4fd84fd4250 *man/summary.Event.Rd
4e93b495eb10f5e32273f047f07204ae *man/summary.F81.Rd
05e61973b21e91967978db4e9ab7e757 *man/summary.F84.Rd
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8bea8962279aaf40840d71587d661652 *man/summary.GTR.Rd
3230abeb7f74f9feeea6fe03ba6e118f *man/summary.GY94.Rd
756bcbedfa7022c1d93014f25a63657e *man/summary.GeneralDeletor.Rd
4bc5398285b2b4f0b61b105c01dadba0 *man/summary.GeneralInDel.Rd
424c737250727f7dab95958b60f4fe1a *man/summary.GeneralInsertor.Rd
605f36cead4761e949619c2c2a49b236 *man/summary.GeneralSubstitution.Rd
6af6e378d17dd6421f51c6c9d3c13d86 *man/summary.HKY.Rd
4bbc31b4302c63f1ade615ff7dbe11f9 *man/summary.JC69.Rd
8d7ada0e28f8fa89d85469311e4ef5c8 *man/summary.K80.Rd
e7e4f71b367b18dca77576bd75dce297 *man/summary.K81.Rd
518e18bcdf5a6d90c870df019301355d *man/summary.PSRoot.Rd
00ab34907457996df1df5e45c497a1ea *man/summary.PhyloSim.Rd
39cad1abb1aa77324d6fb1bbd439768a *man/summary.Process.Rd
0724e58adcc89182dd81fb29eb8ebaee *man/summary.QMatrix.Rd
24a4b09c1e600a6a154260e8165ca43d *man/summary.Sequence.Rd
60bb2e1e0add0d6477503eb7f0a42965 *man/summary.Site.Rd
72815dca092506ef6ecac9c17ff4bb85 *man/summary.T92.Rd
30873272c1770919049249227ea1599d *man/summary.TN93.Rd
108b004eae7821bce1f71706703d085d *man/summary.UNREST.Rd
2f463d7375df7b1e54e097a690b79567 *man/translateCodon.CodonAlphabet.Rd
63adea75ce25365a5a768fea029cec12 *man/virtualAssignmentForbidden.PSRoot.Rd
bf371449807ac728171c01ab4fbe0306 *vignettes/Makefile
1d3e687aec2e6c74f84ddc3dd9af7931 *vignettes/PhyloSim.Rnw
