# Generated by roxygen2: do not edit by hand

export(BuildTree)
export(FindIndel)
export(IndelForm)
export(IndelIdents)
export(IndelPlot)
export(PlotTree)
export(ReadCutsite)
export(ReadFasta)
export(TagDist)
export(TagProcess)
export(align_to_range)
export(change_form_stat)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,score)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,type)
importFrom(BiocGenerics,width)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,alignedPattern)
importFrom(Biostrings,alignedSubject)
importFrom(Biostrings,consensusString)
importFrom(Biostrings,matchPattern)
importFrom(Biostrings,nucleotideSubstitutionMatrix)
importFrom(Biostrings,pairwiseAlignment)
importFrom(Biostrings,pattern)
importFrom(Biostrings,subseq)
importFrom(IRanges,IRanges)
importFrom(IRanges,subject)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,na.omit)
importFrom(ape,rotateConstr)
importFrom(cowplot,plot_grid)
importFrom(data.tree,FromDataFrameNetwork)
importFrom(data.tree,ToDataFrameNetwork)
importFrom(data.tree,ToListExplicit)
importFrom(data.tree,ToNewick)
importFrom(data.tree,as.Node)
importFrom(dplyr,group_by)
importFrom(dplyr,summarise)
importFrom(ggnewscale,new_scale_color)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggtree,geom_facet)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,ggtree)
importFrom(ggtree,read.tree)
importFrom(ggtree,xlim_expand)
importFrom(networkD3,diagonalNetwork)
importFrom(networkD3,saveNetwork)
importFrom(parallel,clusterEvalQ)
importFrom(parallel,clusterExport)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(pheatmap,pheatmap)
importFrom(purrr,"%>%")
importFrom(purrr,map_chr)
importFrom(reshape2,acast)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(rlist,list.insert)
importFrom(rlist,list.order)
importFrom(stats,cor)
importFrom(stats,pnorm)
importFrom(stats,sd)
importFrom(stringdist,stringdistmatrix)
importFrom(stringr,str_extract)
importFrom(stringr,str_extract_all)
