# Generated by roxygen2: do not edit by hand

export(bootstrapTrees)
export(buildIgphyml)
export(buildPML)
export(buildPhylo)
export(buildPratchet)
export(collapseNodes)
export(colorTrees)
export(condenseTrees)
export(correlationTest)
export(createGermlines)
export(downsampleClone)
export(findSwitches)
export(formatClones)
export(getDivergence)
export(getNodeSeq)
export(getPalette)
export(getSeq)
export(getSubclones)
export(getTrees)
export(makeAirrClone)
export(makeModelFile)
export(maskCodons)
export(maskSequences)
export(plotTrees)
export(readFasta)
export(readIMGT)
export(readLineages)
export(readModelFile)
export(reconIgPhyML)
export(rerootTree)
export(resolvePolytomies)
export(scaleBranches)
export(testPS)
export(testSC)
export(testSP)
export(treesToPDF)
export(writeLineageFile)
exportClasses(airrClone)
import(ggplot2)
import(ggtree)
import(graphics)
import(markdown)
import(methods)
import(utils)
importFrom(Biostrings,pairwiseAlignment)
importFrom(alakazam,DNA_IUPAC)
importFrom(alakazam,makeChangeoClone)
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(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,if_else)
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(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(shazam,setRegionBoundaries)
importFrom(stringr,str_count)
importFrom(tidyselect,all_of)
