# Generated by roxygen2: do not edit by hand

S3method(extractSite,fixationSites)
S3method(extractSite,multiFixationSites)
S3method(extractTips,fixationSites)
S3method(extractTips,multiFixationSites)
S3method(extractTips,sitePath)
S3method(fixationSites,lineagePath)
S3method(multiFixationSites,lineagePath)
S3method(plot,lineagePath)
S3method(plot,sitePath)
S3method(plotSingleSite,fixationSites)
S3method(plotSingleSite,lineagePath)
S3method(plotSingleSite,multiFixationSites)
S3method(print,fixationSites)
S3method(print,lineagePath)
S3method(print,multiFixationSites)
S3method(print,sitePath)
S3method(setSiteNumbering,lineagePath)
S3method(setSiteNumbering,phylo)
export(SNPsites)
export(addMSA)
export(extractSite)
export(extractTips)
export(fixationSites)
export(groupTips)
export(lineagePath)
export(multiFixationSites)
export(plotSingleSite)
export(setSiteNumbering)
export(similarityMatrix)
export(sneakPeek)
importFrom(Rcpp,sourceCpp)
importFrom(ape,drop.tip)
importFrom(ape,getMRCA)
importFrom(ape,ladderize)
importFrom(ape,nodepath)
importFrom(ape,plot.phylo)
importFrom(graphics,legend)
importFrom(graphics,plot)
importFrom(graphics,title)
importFrom(methods,is)
importFrom(seqinr,read.alignment)
importFrom(stats,sd)
importFrom(utils,flush.console)
importFrom(utils,setTxtProgressBar)
importFrom(utils,tail)
importFrom(utils,txtProgressBar)
useDynLib(sitePath)
