5c6a48317748df858cda5fef6f38937e *DESCRIPTION
9dcac14a94153218ae029f0407514f46 *NAMESPACE
edd0677b91f93420025f92ccbf366662 *NEWS.md
ba4f165b81f299369fc4454c536bc80e *R/AAHitScoping.R
b6f3addcd0c30c261c7113a36bf940af *R/ApproximateBackground.R
2fcf68e8a8bb767846952ca26adb9cb0 *R/BlastSeqs.R
6b9e3393dab9693b6bf6599f41c9d759 *R/BlockByRank.R
9b3e18d0aa11d470513e72f313e93532 *R/BlockExpansion.R
ecd31e718789f6c19bf5cac908f61dcc *R/BlockReconciliation.R
39055b8931487fb0c0faaad3f69ef6c8 *R/CheckAgainstReport.R
bc2295a76a35f1663341507f9d3702e5 *R/ClusterByK.R
078ebc121fc107a724a116afe41b3bc1 *R/CompetePairs.R
439fcc0d5c05b4dc1b4ac70b109d2deb *R/DPhyloStatistic.R
270fa33338f3125795f1dfce252606b2 *R/DisjointSet.R
c7bb548d6cb5428ccb31ce67a1823dd9 *R/EstimRearrScen.R
a535d8ce8bb3073ecf7c924700dce0c0 *R/EvoWeaver-GOPreds.R
2f48ab34a797beb8c93ae4fb2ff6d97a *R/EvoWeaver-PPPreds.R
31dc7af32650a1bbeb7f226f0b706ad3 *R/EvoWeaver-PSPreds.R
73f6c1d53778c688e1556529ef343a28 *R/EvoWeaver-SLPreds.R
692f2908a372872e2c9fb79eea96204d *R/EvoWeaver-class.R
4fc6849ba0288eb979629da8a252a45d *R/EvoWeaver-utils.R
422b8c851e3af4d32c98afd876dcd878 *R/EvoWeb-class.R
0c2590215402801b6e36b674d92f01a9 *R/ExoLabel.R
496309229a880221262bf4bba3f4e3fe *R/ExpandDiagonal.R
d97f14de38ed10c36b7fb3d249c1de51 *R/ExtractBy.R
1f0d3ed11cdeb3b6bf5a3621d7df4a3d *R/FastDend-class.R
dae108b2bf5cced94a00e075adee017c *R/FastQFromSRR.R
3fa59094c1b69a1f2ba91a6350786a02 *R/FindSets.R
e617ebbbf78d2b9779000dfd3f887825 *R/FitchParsimony.R
26fc80c538ea8dcec352475fc5aab84a *R/HitConsensus.R
740fd56121967ddc7cc7ea7273c5a08b *R/HungarianAssignment.R
d024b41542f877275c9a287f7e954dea *R/LanczosEigen.R
40d5588b64cdeedea9e3d5a4b737e02e *R/LinkedPairs-class.R
e39fae4f15f33a98704033c46aedb9d0 *R/MoranI.R
a47f7a5a9e2c746da9fed9078b8264af *R/NormVec.R
ea8172ccf944875e102f1a0f875a1b80 *R/NucleotideOverlap.R
d14447a8d7a0f89633eea3d3673f740e *R/OneSite.R
592c28a30c8311d1ef05442eaf48c1d4 *R/PairSummaries.R
63962d32dc03a3990db0486c54399e02 *R/PhyloDistance.R
6505f61f375c39f2c984c0e2badb0d7d *R/PrepareSeqs.R
f5fc9fa7df945c4e41dd46849d8f4294 *R/RandForest.R
1c10f95f605feceb847fe82e37249795 *R/RejectionBy.R
b70111e2f543fd36c2453fc9536c6d44 *R/SelectByK.R
d097928081bd83ccf02681696de42b52 *R/SequenceSimilarity.R
1075722f990a1663d63a50c68878f987 *R/ShuffleC.R
0d128904011275f183eeb9e37c1ebdc7 *R/SubSetPairs.R
19b710eb09341f806360849187bd6285 *R/SummarizePairs.R
7cdb2de522ff4c89ba4d201afa287f3e *R/SuperTree.R
9c8d64407bbe81f7d5e78a09a443ae6b *R/WithinSetCompetition.R
391fae531baae490afb642aefa12893e *R/dendrapply.R
285c994bbb16facb1d6e15ad13325350 *R/dineof.R
6df6086b429cb3d0c5e4d295dfb156bc *R/gffToDataFrame.R
b046600f220f3cc67126dc023d83429b *R/simMat-class.R
846bcdb05de633ae7366cf3a89b145e1 *R/subset-dendrogram.R
90989e03d84a62ca9ddcee443214537c *README.md
4ce3ae884d00ba765684934269efc363 *build/vignette.rds
bd9032488b7f5f303678a25a33f15a32 *cleanup
ffd04863ac14a07fe4dcd1d1416ed725 *data/BuiltInEnsembles.RData
a30398c4f8ae9d3c6f69bd151bfb83af *data/CIDist_NullDist.RData
60dc7d72a7d127f0b251921f837949d2 *data/Endosymbionts_GeneCalls.RData
55c8cbeef23ed0527917efafb997fc4f *data/Endosymbionts_Gene_Communities.RData
de9ce5df7b4c31b6dabafe92fca77eab *data/Endosymbionts_LinkedFeatures.RData
19d1ddd8bcf3a96b76d5f712ac2c2d93 *data/Endosymbionts_Pairs01.RData
99df1ea8574ae3231962ca480bf4df47 *data/Endosymbionts_Pairs02.RData
99ccfc6196f61ce109a0a4216e76e910 *data/Endosymbionts_Pairs03.RData
b349e0b52359349fc8586a6ea11f2955 *data/Endosymbionts_Sets.RData
1549635e4573b3fb011a1b6842775ace *data/Endosymbionts_Synteny.RData
361fad3c30cd73230e810fafa13054d1 *data/ExampleStreptomycesData.RData
911601b6d0aa525e19a9eabacbbedd8f *data/Generic.RData
ff60bae67e61d99bdc3665ceb475ea36 *data/SuperTreeEx.RData
0fa0dcf19953d32d45de08a5d978f7dd *data/datalist
e76d7f40fcf212f10ba543438a013ec9 *inst/doc/UsingSynExtend.R
a7f9ffe6b33c9ddf518710c490a30e51 *inst/doc/UsingSynExtend.Rmd
d5a6b3b02d747b8243e0755468cf21b1 *inst/doc/UsingSynExtend.html
e36097aba877f5d88846679804556664 *inst/extdata/Endosymbionts_v05a.sqlite
6674fb70844eca54d5765083f8838061 *inst/extdata/GCF_023585825.1_ASM2358582v1_genomic.gff.gz
e4f68129ca2b999163dd563a07ec4bbf *inst/scripts/extdata.R
17e0edc4a57af404aa668ef231769c12 *man/AAHitScoping.Rd
515c623912d59e1e225b792de7aad8ff *man/ApproximateBackground.Rd
0e980cbc4994ff8c88bbc511dade41ea *man/BlastSeqs.Rd
25abf9d378d77cd10cde5bab145f4753 *man/BlockByRank.Rd
6adb109fa7bf2af21281930172c13454 *man/BlockExpansion.Rd
ccfd2d587743f4aff4d21be064631629 *man/BlockReconciliation.Rd
8339a92f8519b8e76fe8fc1c4d92abc4 *man/BuiltInEnsembles.Rd
8f87fcd9ecc112dcc123f4708d1358fc *man/CIDist_NullDist.Rd
8d51a8ecfeff9fea27c89d6b054a0752 *man/CheckAgainstReport.Rd
ce113d6b91a5dc819e977b05b356f791 *man/ClusterByK.Rd
7f4acf398ddcc0c357eb995e84fa2ac7 *man/CompetePairs.Rd
e76258e0ed7aae0a5522fe7b04f9745d *man/DPhyloStatistic.Rd
976360434a04771cf944d4c1258a5bc4 *man/DecisionTree-class.Rd
dd2c8667bcd9ee1ee19b0156d2ffa6c9 *man/DisjointSet.Rd
2643ddfea4519c2e870ad9cce719ae94 *man/Endosymbionts_GeneCalls.Rd
7c834c9c2f65c7e423a59eceadb10101 *man/Endosymbionts_LinkedFeatures.Rd
aea651f67ce1e421b71a53b55b9b262f *man/Endosymbionts_Pairs01.Rd
d00132d6f9f7e9a5c63ecec1fad07e00 *man/Endosymbionts_Pairs02.Rd
aa56ba754ebed7bd02622f4a06394e17 *man/Endosymbionts_Pairs03.Rd
285ca7b16c3154dd9e3dc6f54dd0f7fb *man/Endosymbionts_Sets.Rd
26e8c11bd794eead59aa446c8437a883 *man/Endosymbionts_Synteny.Rd
3ab00e8c283b45c621bee1d40b55642e *man/EstimRearrScen.Rd
0a29d9c4e20cab2ac7d21f435bbcf054 *man/EstimateExoLabel.Rd
ea3eb8bf58ddea4a083e141300d991d4 *man/EvoWeaver-GOPreds.Rd
4d1675e791ba4b88656dda5a58ec407c *man/EvoWeaver-PPPreds.Rd
23ea0a0486bb0e405777730a204a70ae *man/EvoWeaver-PSPreds.Rd
fd8693c50114b1a46cea5b963f1502c2 *man/EvoWeaver-SLPreds.Rd
394579a8f12607fcdc6b926aeb5fe8d0 *man/EvoWeaver.Rd
6992276799143fe1845402eabea9010c *man/EvoWeb.Rd
ea27731062b703725fab560a7123feda *man/ExampleStreptomycesData.Rd
24d5ec949669b77e9c5fa03cd62c3367 *man/ExoLabel.Rd
9ca0902dc6b570e00bbf71f401a48857 *man/ExpandDiagonal.Rd
75b4a299def7cdd3408d3025ee4a8d48 *man/ExtractBy.Rd
b707662154e8bdbc3b6c6b083171c9f9 *man/FastQFromSRR.Rd
c81f47efbae1fd1870245f766c4f6bbf *man/FindSets.Rd
b5b735e0453c50d6220f3ace934d9350 *man/FitchParsimony.Rd
d5488ce72a0a1110cfc070880c07739d *man/Generic.Rd
95176c3e3f438c94407ab735826ed714 *man/HitConsensus.Rd
d4fee6de63636cc9e557b26861bde664 *man/LinkedPairs-class.Rd
84918477bd78ac1b5b047e0cec4f6b24 *man/MakeBlastDb.Rd
483018d84f868b1e5eb602655e133a28 *man/MoransI.Rd
7e596d172fb6a09e8070f3b8ad393ffc *man/NormVec.Rd
689ed80e69fd0f77e6c6357fa92817bd *man/NucleotideOverlap.Rd
011fb9dec0002112a6e7c00df47b5b24 *man/OneSite.Rd
80e00fd7721ab9a0c1753b49fee92a02 *man/PairSummaries.Rd
83e5f7f6f5d0508bab06657a551db55c *man/PhyloDistance-CI.Rd
2132774fd6fa26c771aa219225c5b7c7 *man/PhyloDistance-JRF.Rd
f042997ae6ea3d1af2798c34b69542aa *man/PhyloDistance-KF.Rd
de728908d0d0dc93ebb93d07b58723dc *man/PhyloDistance-RF.Rd
e30e844fe816bf45629e7cc536cbed9d *man/PhyloDistance.Rd
cb28718e1f39ed898b3e70288ba11964 *man/PrepareSeqs.Rd
eeba6a3b79c95046edf59442de53da95 *man/RandForest.Rd
2b3cc1679834a305510957394877fca1 *man/RejectionBy.Rd
9d9fe88ceecf7170f6ff2864dd3a1291 *man/SelectByK.Rd
6a51e1a396fe12a114778dec1f49e837 *man/SequenceSimilarity.Rd
ece691cca78bed7f32fe7919acac5ac1 *man/SubSetPairs.Rd
807032b83c6e457020ac11c83b7af0c9 *man/SummarizePairs.Rd
4d1e04d7b7cf6bf90f209b84f0213990 *man/SuperTree.Rd
c2ff665437c83a3e3d9bb20293c5f496 *man/SuperTreeEx.Rd
5367d28173006d1408f139149b8d94a1 *man/WithinSetCompetition.Rd
f5079a675ef56c7a35385423daa13470 *man/dendrapply.Rd
6cbbeb4ced460fe8eca328fe7628744f *man/gffToDataFrame.Rd
28dc4757fe7b6df995cfb895d1a38f17 *man/plot.EvoWeb.Rd
a99a9ad8672efad26c921156dd5b560e *man/predict.EvoWeaver.Rd
eff02199ee0a7be3c0bef7d401e98d5b *man/simMat.Rd
02c3285076ad2671625a058a0ba1418c *man/subset-dendrogram.Rd
2254faf65c17395247ac99805980cd33 *src/CDend.c
640dc86cc19d1e16fad2c228840f0687 *src/CDend.h
123312f18293f7f488f405069b228b75 *src/CShuffle.c
337684423742277e72d5abda77f94891 *src/ExoLabel/ExoLabel.c
e093dc464b5d36f76176d3fef3f23b3e *src/ExoLabel/ExoLabel.h
89439108627940e68a863c59304a68f0 *src/ExoLabel/FallbackDefines.h
7a2e8707184b3359c39e279d37a117bd *src/ExoLabel/FileHandlers.c
2ec960db01627c2e46c458b222e775a6 *src/ExoLabel/FileHandlers.h
3614c137102d3fe36886e90cd4d6339c *src/ExoLabel/LoserTree.c
ca8353512bf0db232d935e9e58f13731 *src/ExoLabel/LoserTree.h
2451eb3cfd87ce03328fe5228490efde *src/ExoLabel/PrefixTrie.c
d1e4c5c7fce9028e6d37fe6003a01172 *src/ExoLabel/PrefixTrie.h
41bfb6441575ed3f2e6fc21316a518af *src/HitConsensus.c
f1455d1dccbd99d549403d2daec90fe8 *src/HungarianAlgo.c
b43ef81ed478db7a52aeefca3609c967 *src/HungarianAlgo.h
eccc6519286e8beabf8b44ac19ba8803 *src/Makevars
05fb85070ac744944ce8b2c7edee797c *src/MoranI.c
30fb5fab97caed0103c0c6c827c718de *src/NucleotideCounts.c
f958b12d19d448712227b5bea16da116 *src/R_init_synextend.c
eb04e6069fd0884896df5b76ac1a753f *src/RandomForest.c
4f9bcf9fa9b4019c0536b8b312321ed0 *src/RandomForest.h
4d501a13764893ad57868ae544ac7889 *src/SEutils.c
b8962521f7a0dc7b1b19d8215e078291 *src/SEutils.h
fe228614e8bc917ce696d687691268b7 *src/SynExtend.h
101e08b40d655cc6a4fb3d8d506ce31a *src/XORRand.c
1ac5feb07e61417d0ca74d7bd646f583 *src/calcMIR2C.c
455dae1f0d842ce62a9732b1cf03160d *src/cart_methods.f95
ab17f188e47e63da5ed1d25aed23fe8b *src/dendrapply.c
3a2aa7628132e5ba0021ccdb372edd8c *src/fortran_includes.h
a23c766f0674921de364fa5465c0b4b3 *src/tabulate_mod.f95
06890049eee7cb3fd058bcf7b4a452a4 *src/utilfuncs.f95
9dd65e40b45944e0187ab857943d251b *tests/check_ExoLabel_compression.c
001448a2015eecea99dc6bff0aeb1e01 *tests/test_ExoLabel.R
a7f9ffe6b33c9ddf518710c490a30e51 *vignettes/UsingSynExtend.Rmd
