# Generated by roxygen2: do not edit by hand

S3method(SNPsites,phyMSAmatched)
S3method(addMSA,phylo)
S3method(addMSA,treedata)
S3method(allSitesName,SNPsites)
S3method(allSitesName,fixationSites)
S3method(allSitesName,paraFixSites)
S3method(allSitesName,parallelSites)
S3method(allSitesName,sitesMinEntropy)
S3method(as.data.frame,SNPsites)
S3method(as.data.frame,fixationSites)
S3method(as.data.frame,parallelSites)
S3method(as.phylo,fixationSites)
S3method(as.phylo,phyMSAmatched)
S3method(as.phylo,sitePath)
S3method(as.phylo,sitesMinEntropy)
S3method(as.treedata,fixationPath)
S3method(as.treedata,fixationSites)
S3method(extractSite,fixationSites)
S3method(extractSite,parallelSites)
S3method(extractTips,fixationSites)
S3method(extractTips,lineagePath)
S3method(extractTips,parallelSites)
S3method(extractTips,sitePara)
S3method(extractTips,sitePath)
S3method(extractTips,sitesMinEntropy)
S3method(fixationIndels,sitesMinEntropy)
S3method(fixationPath,fixationSites)
S3method(fixationPath,sitesMinEntropy)
S3method(fixationSites,lineagePath)
S3method(fixationSites,paraFixSites)
S3method(fixationSites,sitesMinEntropy)
S3method(groupTips,fixationPath)
S3method(groupTips,fixationSites)
S3method(groupTips,lineagePath)
S3method(groupTips,phyMSAmatched)
S3method(groupTips,sitesMinEntropy)
S3method(lineagePath,paraFixSites)
S3method(lineagePath,phyMSAmatched)
S3method(lineagePath,phylo)
S3method(lineagePath,sneakPeekedPaths)
S3method(lineagePath,treedata)
S3method(multiFixationSites,lineagePath)
S3method(paraFixSites,lineagePath)
S3method(paraFixSites,phylo)
S3method(paraFixSites,sitesMinEntropy)
S3method(paraFixSites,treedata)
S3method(parallelSites,lineagePath)
S3method(parallelSites,paraFixSites)
S3method(parallelSites,sitesMinEntropy)
S3method(plot,fixationPath)
S3method(plot,fixationSites)
S3method(plot,lineagePath)
S3method(plot,parallelSites)
S3method(plot,phyMSAmatched)
S3method(plot,sitePath)
S3method(plotFixationSites,fixationSites)
S3method(plotFixationSites,paraFixSites)
S3method(plotMutSites,SNPsites)
S3method(plotMutSites,fixationSites)
S3method(plotMutSites,lineagePath)
S3method(plotMutSites,paraFixSites)
S3method(plotMutSites,parallelSites)
S3method(plotParallelSites,paraFixSites)
S3method(plotParallelSites,parallelSites)
S3method(plotSingleSite,fixationSites)
S3method(plotSingleSite,lineagePath)
S3method(plotSingleSite,parallelSites)
S3method(plotSingleSite,sitesMinEntropy)
S3method(print,SNPsites)
S3method(print,alignment)
S3method(print,fixationIndels)
S3method(print,fixationPath)
S3method(print,fixationSites)
S3method(print,indelPath)
S3method(print,lineagePath)
S3method(print,paraFixSites)
S3method(print,parallelSites)
S3method(print,phyMSAmatched)
S3method(print,sitePara)
S3method(print,sitePath)
S3method(print,sitesMinEntropy)
S3method(setSiteNumbering,phyMSAmatched)
S3method(sitesMinEntropy,lineagePath)
export(SNPsites)
export(addMSA)
export(allSitesName)
export(as.phylo)
export(as.treedata)
export(extractSite)
export(extractTips)
export(fixationIndels)
export(fixationPath)
export(fixationSites)
export(groupTips)
export(lineagePath)
export(multiFixationSites)
export(paraFixSites)
export(parallelSites)
export(plotFixationSites)
export(plotMutSites)
export(plotParallelSites)
export(plotSingleSite)
export(read.alignment)
export(read.tree)
export(setSiteNumbering)
export(similarityMatrix)
export(sitesMinEntropy)
export(sneakPeek)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rcpp,sourceCpp)
importFrom(ape,Nnode)
importFrom(ape,Ntip)
importFrom(ape,as.phylo)
importFrom(ape,getMRCA)
importFrom(ape,is.binary)
importFrom(ape,multi2di)
importFrom(ape,node.depth.edgelength)
importFrom(ape,nodepath)
importFrom(ape,read.tree)
importFrom(aplot,insert_left)
importFrom(ggplot2,GeomPoint)
importFrom(ggplot2,GeomSegment)
importFrom(ggplot2,GeomText)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,theme)
importFrom(ggrepel,geom_label_repel)
importFrom(ggtree,geom_point2)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,ggtree)
importFrom(ggtree,theme_tree2)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,plot)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(methods,is)
importFrom(parallel,clusterSplit)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(seqinr,read.alignment)
importFrom(stats,complete.cases)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(tidytree,as.treedata)
importFrom(tidytree,as_tibble)
importFrom(tidytree,full_join)
importFrom(tidytree,groupOTU)
importFrom(utils,flush.console)
importFrom(utils,head)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
useDynLib(sitePath)
