# Generated by roxygen2: do not edit by hand

export(bootstrapTrees)
export(buildAllClonalGermlines)
export(buildBeast)
export(buildIgphyml)
export(buildPML)
export(buildPhylo)
export(buildPratchet)
export(buildRAxML)
export(calcRF)
export(checkDivergence)
export(checkNodeDivergences)
export(collapseNodes)
export(colorTrees)
export(condenseTrees)
export(correlationTest)
export(createAllGermlines)
export(createGermlines)
export(dfToFasta)
export(downsampleClone)
export(dowserObjectEquivalent)
export(exportTrees)
export(filterCombs)
export(filterPartialSeqs)
export(findSwitches)
export(formatClones)
export(getAllSeqs)
export(getBootstraps)
export(getDiffPoints)
export(getDivergence)
export(getNodeSeq)
export(getPalette)
export(getSeq)
export(getSeqPath)
export(getSkylines)
export(getSubTaxa)
export(getSubclones)
export(getTimeTrees)
export(getTimeTreesIterate)
export(getTrees)
export(getTreesAndUCAs)
export(makeAirrClone)
export(makeModelFile)
export(makeSkyline)
export(mapSubtrees)
export(maskCodons)
export(maskSequences)
export(plotMSA)
export(plotSkylines)
export(plotTrees)
export(readBEAST)
export(readFasta)
export(readIMGT)
export(readLineages)
export(readModelFile)
export(readTreesJSON)
export(reconIgPhyML)
export(rerootTree)
export(resolveLightChains)
export(resolvePolytomies)
export(sampleClones)
export(scaleBranches)
export(setNodeDivergences)
export(testPS)
export(testSC)
export(testSP)
export(treesEquivalent)
export(treesToPDF)
export(writeCloneSequences)
export(writeFasta)
export(writeLineageFile)
export(writeTreesJSON)
exportClasses(airrClone)
import(ggplot2)
import(ggtree)
import(graphics)
import(markdown)
import(methods)
import(utils)
importFrom(airr,read_rearrangement)
importFrom(alakazam,DNA_IUPAC)
importFrom(alakazam,buildPhylipLineage)
importFrom(alakazam,checkColumns)
importFrom(alakazam,collapseDuplicates)
importFrom(alakazam,getAllele)
importFrom(alakazam,getGene)
importFrom(alakazam,graphToPhylo)
importFrom(alakazam,makeTempDir)
importFrom(alakazam,maskSeqGaps)
importFrom(alakazam,padSeqEnds)
importFrom(alakazam,seqDist)
importFrom(alakazam,translateDNA)
importFrom(ape,as.AAbin)
importFrom(ape,as.DNAbin)
importFrom(ape,bind.tree)
importFrom(ape,collapse.singles)
importFrom(ape,di2multi)
importFrom(ape,dist.nodes)
importFrom(ape,extract.clade)
importFrom(ape,getMRCA)
importFrom(ape,is.rooted)
importFrom(ape,keep.tip)
importFrom(ape,ladderize)
importFrom(ape,multi2di)
importFrom(ape,read.dna)
importFrom(ape,read.tree)
importFrom(ape,reorder.phylo)
importFrom(ape,root)
importFrom(ape,subtrees)
importFrom(ape,unroot)
importFrom(coda,HPDinterval)
importFrom(coda,as.mcmc)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,combine)
importFrom(dplyr,desc)
importFrom(dplyr,do)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_at)
importFrom(dplyr,n)
importFrom(dplyr,one_of)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,right_join)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarize)
importFrom(dplyr,summarize_at)
importFrom(dplyr,transmute)
importFrom(dplyr,ungroup)
importFrom(gridExtra,grid.arrange)
importFrom(jsonlite,read_json)
importFrom(jsonlite,write_json)
importFrom(phangorn,NJ)
importFrom(phangorn,acctran)
importFrom(phangorn,ancestral.pars)
importFrom(phangorn,ancestral.pml)
importFrom(phangorn,dist.ml)
importFrom(phangorn,optim.pml)
importFrom(phangorn,phyDat)
importFrom(phangorn,pml)
importFrom(phangorn,pml.control)
importFrom(phangorn,pratchet)
importFrom(phylotate,read_annotated)
importFrom(pwalign,pairwiseAlignment)
importFrom(shazam,setRegionBoundaries)
importFrom(stringr,str_count)
importFrom(tidyselect,all_of)
importFrom(treeio,read.beast)
importFrom(utils,packageDescription)
