Protein Sequences

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BEND3RER.nwk

DESCRIPTION

Downloading

LICENSE

NAMESPACE

NoncodingRegionWorkflow

R/PermulationFuncs.R R/RERfuncs.R R/RcppExports.R R/asr_diagnostics.R R/coordsfn.R R/enrichmentFuncs.R R/estimateTreeFuncs.R R/plottingFuncs.R R/projection_coevo.R README.md RERconverge-master.pdf

RERconverge.Rproj

Rplots.pdf

data/RERresults.RData

data/basalRate.RData

data/logAdultWeightcm.RData

data/mamRERw.RData

data/mamTreesSub.RData

data/marineBinary.RData

data/marineTreesSub.RData

data/sleepPattern.RData

data/toyTrees.RData

ext/ExampleAlignments/APOE.fasta

ext/ExampleAlignments/EGFR.fasta

ext/ExampleAlignments/TNF.fasta

ext/ExampleAlignments/TP53.fasta

ext/ExampleAlignments/VEGFA.fasta

ext/MammalToyTrees.txt

ext/MarineGeneTrees.tre

ext/MarineTreeBin.txt

ext/MarineTreeBinCommonNames.txt

ext/MarineTreeBinCommonNames_noCGM.txt

ext/OriginalUpdatedRERsMoleAccelerationPrecisionRecall.rds

ext/eyespecificgenes.master.list

ext/mammal62aa_meredplus_wCM.trees

ext/mammal_62_aa_sub.tre

ext/mastertree.tree

ext/speciesCommonAbbr.name

ext/subsetMammalGeneTrees.txt

gmtfile.gmt

inst/extdata/ExampleAlignments/APOE.fasta

inst/extdata/ExampleAlignments/EGFR.fasta

inst/extdata/ExampleAlignments/TNF.fasta

inst/extdata/ExampleAlignments/TP53.fasta

inst/extdata/ExampleAlignments/VEGFA.fasta

inst/extdata/MammalToyTrees.txt

inst/extdata/MarineTreeBin.txt

inst/extdata/MarineTreeBinCommonNames.txt

inst/extdata/MarineTreeBinCommonNames_noCGM.txt

inst/extdata/mammal_62_aa_sub.tre

inst/extdata/mastertree.tree

inst/extdata/subsetMammalGeneTrees.txt

mamRERw.rds

man/RERconverge.Rd man/Root.Rd man/adaptivePermulation.Rd man/asymmRerootingMethod.Rd man/boxPlotTest.Rd man/calculateCorPermuted.Rd man/calculatePermulatedPaths_apply.Rd man/char2Paths.Rd man/char2PathsCategorical.Rd man/char2TreeCategorical.Rd man/click_select_foreground_branches.Rd man/combinePermData.Rd man/compareRateModels.Rd man/correlateWithBinaryPhenotype.Rd man/correlateWithCategoricalPhenotype.Rd man/correlateWithContinuousPhenotype.Rd man/edgeVars.Rd man/estimatePhangornTree.Rd man/estimatePhangornTreeAll.Rd man/fastwilcoxGMTall.Rd man/filterByCriteria.Rd man/fixPseudoroot.Rd man/foreground2Paths.Rd man/foreground2Tree.Rd man/foreground2TreeClades.Rd man/generatePermulatedBinPhen.Rd man/generatePermulatedBinPhenSSMBatched.Rd man/getAllCor.Rd man/getAllCorExtantOnly.Rd man/getAllResiduals.Rd man/getAncLiks.Rd man/getBinaryPermulationInputsFromTree.Rd man/getEnrichPerms.Rd man/getForegroundInfoClades.Rd man/getLRnullDistribution.Rd man/getLikelihoodRatio.Rd man/getMatrixFromAbbr.Rd man/getPermsBinary.Rd man/getPermsBinaryExtantOnly.Rd man/getPermsContinuous.Rd man/getPermsContinuousExtantOnly.Rd man/getStat.Rd man/getStatesAtNodes.Rd man/getStatesFromPhenTree.Rd man/kwdunn.test.Rd man/makeBinaryPaths.Rd man/matchAllNodesClades.Rd man/namePathsWSpecies.Rd man/permpvalcor.Rd man/permpvalenrich.Rd man/permutevec.Rd man/plotPositivesFromPermulations.Rd man/plotRers.Rd man/plotTreeCategorical.Rd man/plotTreeHighlightBranches.Rd man/pruneTree.Rd man/read.gmt.Rd man/readTrees.Rd man/returnRersAsNewickStrings.Rd man/returnRersAsTree.Rd man/returnRersAsTreesAll.Rd man/searchRateModels.Rd man/simBinPheno.Rd man/simBinPhenoCC.Rd man/simBinPhenoCCmidpoint.Rd man/simBinPhenoRank.Rd man/simBinPhenoSSM.Rd man/simBinPhenoVec.Rd man/simpermvec.Rd man/simulatevec.Rd man/tree2Paths.Rd man/tree2PathsClades.Rd man/treePlotNew.Rd man/treePlotRers.Rd man/visCompareTwoRateModels.Rd new_plotTreeHighlightBranches.R

src/Makevars

src/Makevars.win

src/RERconverge.dll

src/RcppExports.cpp

src/resid.cpp

tests/CheckTree2Paths.R tests/ConvertSpeciesNames.R

tests/PON1_addl_species.tre

tests/SpeciesNameConversionTable0818.csv

tests/SpeciesNames.RData

tests/benchmarkRERmethods.R tests/checkTreeMatch.R

tests/herbivoreTest.RData

tests/herbivoreTest.pdf tests/herbivoreTest_al_wt_an_te.pdf tests/herbivoreTest_allOptions.pdf tests/herbivoreTest_anctermOptions.pdf tests/runMarineSub-003.pdf tests/runMarineSub.R

tests/runMarineSub.Rnw

tests/runMarineSub.pdf tests/testBinaryPermulations.R

tests/toyRERs.nwk

tests/ucsc62mammals_commonnames.tre

tests/ucscTrees.RData

toyRERs.nwk

vignettes/ASR-walkthrough.Rmd vignettes/ASR-walkthrough.pdf

vignettes/ASR-walkthrough_cache/latex/__packages

vignettes/BEND3RER.nwk

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nclark-lab/RERconverge documentation built on Feb. 4, 2025, 8:38 a.m.

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nclark-lab/RERconverge
Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

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Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

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