6eaae929cef2423e90372ff2f8344534 *DESCRIPTION
423f7b2114999ddc336abcdb6ccbcf60 *NAMESPACE
b6045b8347bacdf6a8941c750a32639a *NEWS.md
ba4f165b81f299369fc4454c536bc80e *R/AAHitScoping.R
b6f3addcd0c30c261c7113a36bf940af *R/ApproximateBackground.R
2fcf68e8a8bb767846952ca26adb9cb0 *R/BlastSeqs.R
6b9e3393dab9693b6bf6599f41c9d759 *R/BlockByRank.R
39055b8931487fb0c0faaad3f69ef6c8 *R/CheckAgainstReport.R
ce88f527684b47810ad1fe416add656f *R/CreateDecoys.R
439fcc0d5c05b4dc1b4ac70b109d2deb *R/DPhyloStatistic.R
270fa33338f3125795f1dfce252606b2 *R/DisjointSet.R
c7bb548d6cb5428ccb31ce67a1823dd9 *R/EstimRearrScen.R
08ea434f370946303f03490ebc267b2a *R/EvaluatePairs.R
a535d8ce8bb3073ecf7c924700dce0c0 *R/EvoWeaver-GOPreds.R
2f48ab34a797beb8c93ae4fb2ff6d97a *R/EvoWeaver-PPPreds.R
31dc7af32650a1bbeb7f226f0b706ad3 *R/EvoWeaver-PSPreds.R
73f6c1d53778c688e1556529ef343a28 *R/EvoWeaver-SLPreds.R
fd84cc63912c755010dd2baa6b1aa32e *R/EvoWeaver-class.R
4fc6849ba0288eb979629da8a252a45d *R/EvoWeaver-utils.R
422b8c851e3af4d32c98afd876dcd878 *R/EvoWeb-class.R
0c2590215402801b6e36b674d92f01a9 *R/ExoLabel.R
d97f14de38ed10c36b7fb3d249c1de51 *R/ExtractBy.R
1f0d3ed11cdeb3b6bf5a3621d7df4a3d *R/FastDend-class.R
dae108b2bf5cced94a00e075adee017c *R/FastQFromSRR.R
2e6194c255933655651ad75dbfe839a2 *R/FeaturesFromDF.R
3fa59094c1b69a1f2ba91a6350786a02 *R/FindSets.R
e617ebbbf78d2b9779000dfd3f887825 *R/FitchParsimony.R
c8ad08a915e9ee227e38468c29da0794 *R/FrameDownward.R
6c9873b52341a0d5eb0033fa325f4241 *R/GetTranslatedFeatures.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
953086c4994fb74c1c918992b4c6aa06 *R/NucleotideOverlap.R
d14447a8d7a0f89633eea3d3673f740e *R/OneSite.R
63962d32dc03a3990db0486c54399e02 *R/PhyloDistance.R
f5fc9fa7df945c4e41dd46849d8f4294 *R/RandForest.R
1c10f95f605feceb847fe82e37249795 *R/RejectionBy.R
d097928081bd83ccf02681696de42b52 *R/SequenceSimilarity.R
1075722f990a1663d63a50c68878f987 *R/ShuffleC.R
b56520238d792b1b903bcfc37cdbe3b7 *R/SquaregffBy.R
34159ad0ff13f4d6fcdd7cee29376fb8 *R/SummarizePairs.R
7cdb2de522ff4c89ba4d201afa287f3e *R/SuperTree.R
1dc49c0b5282a134ef5c5aa0d504bfe6 *R/ToFeatureSpace.R
391fae531baae490afb642aefa12893e *R/dendrapply.R
285c994bbb16facb1d6e15ad13325350 *R/dineof.R
b046600f220f3cc67126dc023d83429b *R/simMat-class.R
846bcdb05de633ae7366cf3a89b145e1 *R/subset-dendrogram.R
90989e03d84a62ca9ddcee443214537c *README.md
4d57f0b1a86909c2755dbc678d564fa4 *build/vignette.rds
bd9032488b7f5f303678a25a33f15a32 *cleanup
ffd04863ac14a07fe4dcd1d1416ed725 *data/BuiltInEnsembles.RData
a30398c4f8ae9d3c6f69bd151bfb83af *data/CIDist_NullDist.RData
361fad3c30cd73230e810fafa13054d1 *data/ExampleStreptomycesData.RData
911601b6d0aa525e19a9eabacbbedd8f *data/Generic.RData
ff60bae67e61d99bdc3665ceb475ea36 *data/SuperTreeEx.RData
599a373eb67730ccaaa750b48da278cd *data/datalist
5f7d6a6df5aefcad31ddabaf5528e0ec *data/genecalls.RData
93447e6fec2090661504d163e3447bef *data/init_pairs.RData
0c35642555cb4af4c8e94019f63390c0 *data/linked_features.RData
c2a534ecd6635813d5b89601331a1490 *data/syn.RData
5badcf513204b360e60b6ca18e74ea04 *inst/doc/UsingSynExtend.R
52f154475c33b400ea97dbaa152ebff8 *inst/doc/UsingSynExtend.Rmd
8d8d90591f415caa7ab1cf3350e21f4c *inst/doc/UsingSynExtend.html
91a0e9714d79887e958648fbe4500a67 *inst/extdata/GCF_023585725.1_ASM2358572v1_genomic.gff.gz
73eb63cc83d7196abc463a8a7463a31a *inst/extdata/example_db.sqlite
18800324f0375aac2c3fe6797bf4ec62 *inst/scripts/extdata.R
91123940109729caae4572931df08854 *man/AAHitScoping.Rd
515c623912d59e1e225b792de7aad8ff *man/ApproximateBackground.Rd
0e980cbc4994ff8c88bbc511dade41ea *man/BlastSeqs.Rd
3f01571e1e2f68f48372bdd7016b7fcf *man/BlockByRank.Rd
8339a92f8519b8e76fe8fc1c4d92abc4 *man/BuiltInEnsembles.Rd
8f87fcd9ecc112dcc123f4708d1358fc *man/CIDist_NullDist.Rd
8d51a8ecfeff9fea27c89d6b054a0752 *man/CheckAgainstReport.Rd
4e614131b2fb9af443c193c624279b13 *man/CreateDecoys.Rd
e76258e0ed7aae0a5522fe7b04f9745d *man/DPhyloStatistic.Rd
976360434a04771cf944d4c1258a5bc4 *man/DecisionTree-class.Rd
9d610fb21f51d31caa4312c6f5b8bc7a *man/DisjointSet.Rd
3ab00e8c283b45c621bee1d40b55642e *man/EstimRearrScen.Rd
0a29d9c4e20cab2ac7d21f435bbcf054 *man/EstimateExoLabel.Rd
ce4b72662c7937de26c343a169653824 *man/EvaluatePairs.Rd
8dda13889351160b19a0ae6a2f0b16ee *man/EvoWeaver-GOPreds.Rd
7561e07ab5e0e083b0c8b81ff61cfdd8 *man/EvoWeaver-PPPreds.Rd
eae5683fd05d8a3938287e07377e881b *man/EvoWeaver-PSPreds.Rd
541cfaac9fcec9c8f9a0dc788f27eef2 *man/EvoWeaver-SLPreds.Rd
394579a8f12607fcdc6b926aeb5fe8d0 *man/EvoWeaver.Rd
6992276799143fe1845402eabea9010c *man/EvoWeb.Rd
ea27731062b703725fab560a7123feda *man/ExampleStreptomycesData.Rd
24d5ec949669b77e9c5fa03cd62c3367 *man/ExoLabel.Rd
f603b81dbad8f3b617570322d4c2b402 *man/ExtractBy.Rd
b707662154e8bdbc3b6c6b083171c9f9 *man/FastQFromSRR.Rd
3de3317aa712976d1d539ca66e4d82ae *man/FeaturesFromDF.Rd
a0fc4bf8a4feb0fbbddabd68de5566df *man/FindSets.Rd
b5b735e0453c50d6220f3ace934d9350 *man/FitchParsimony.Rd
033007518d24b065d2c97279367ccbbc *man/FrameDownward.Rd
d5488ce72a0a1110cfc070880c07739d *man/Generic.Rd
c09c9724c7d165114825de5da69473cc *man/GetTranslatedFeatures.Rd
aeffeb7d041b694912f13e7899de74dd *man/HitConsensus.Rd
b74a1caf00b154ceb58e12e1a436a566 *man/LinkedPairs-class.Rd
84918477bd78ac1b5b047e0cec4f6b24 *man/MakeBlastDb.Rd
483018d84f868b1e5eb602655e133a28 *man/MoransI.Rd
60f87242f246e15dd38b86e6c9e6f026 *man/NormVec.Rd
1f6de0a29dfed25f8d2159a00b990481 *man/NucleotideOverlap.Rd
725930e5bded374e969ad906a8c82a20 *man/OneSite.Rd
6063fa69af1bb45f301e5a846e5e2417 *man/PhyloDistance-CI.Rd
2132774fd6fa26c771aa219225c5b7c7 *man/PhyloDistance-JRF.Rd
f042997ae6ea3d1af2798c34b69542aa *man/PhyloDistance-KF.Rd
de728908d0d0dc93ebb93d07b58723dc *man/PhyloDistance-RF.Rd
e30e844fe816bf45629e7cc536cbed9d *man/PhyloDistance.Rd
eeba6a3b79c95046edf59442de53da95 *man/RandForest.Rd
6a51e1a396fe12a114778dec1f49e837 *man/SequenceSimilarity.Rd
fd7503479c8990ed7aedf4cc557f67ea *man/SquaregffBy.Rd
f54f5433db17b232f5a657a188bad50d *man/SummarizePairs.Rd
9a896441c8e53b2175b0887ad56e149e *man/SuperTree.Rd
c2ff665437c83a3e3d9bb20293c5f496 *man/SuperTreeEx.Rd
a87c9329a12917faa6eb5c079dec75df *man/ToFeatureSpace.Rd
f5079a675ef56c7a35385423daa13470 *man/dendrapply.Rd
106ed8d127e481fc2904d78bb9962af4 *man/genecalls.Rd
d71afbf23f9780a9431d6a6bab27b88e *man/init_pairs.Rd
1b0f9736c7e901f6aec01248f41f7661 *man/linked_features.Rd
28dc4757fe7b6df995cfb895d1a38f17 *man/plot.EvoWeb.Rd
a99a9ad8672efad26c921156dd5b560e *man/predict.EvoWeaver.Rd
eff02199ee0a7be3c0bef7d401e98d5b *man/simMat.Rd
02c3285076ad2671625a058a0ba1418c *man/subset-dendrogram.Rd
c0910995c7d32b8ead4c8146f53b4796 *man/syn.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
52f154475c33b400ea97dbaa152ebff8 *vignettes/UsingSynExtend.Rmd
