# Export all names
export(
  qvalues,
  assoctuple,
  SeqFeatR_GUI,
  assocpoint,
  assocpointhierarchical,
  foundereffectfinder,
  assocpointpair,
  rewritetuple,
  assocpairfeat,
  visualizepairfeat,
  visualizepair,
  assocpair,
  tartan,
  orPlot,
  comparewithancestral,
  smallmanhattan,
  getfreqs,
  volcanoplot
)

# Import all packages listed as Imports or Depends
import(
  tcltk,
  tcltk2,
  plotrix,
  ggplot2,
  Biostrings,
  R2jags
)

# Import smaller dependencies
importFrom("plyr", "adply")
importFrom("phangorn", "Ancestors")
importFrom("phangorn", "read.phyDat")
importFrom("phangorn", "pml")
importFrom("phangorn", "ancestral.pars")
importFrom("qvalue", "qvalue")
importFrom("widgetTools", "dropdownList")
importFrom("calibrate", "textxy")
importFrom("coda", "as.mcmc")
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "rgb")
importFrom("scales", "trans_new", "log_breaks", "trans_breaks", "trans_format", "math_format")
importFrom("graphics", "abline", "axis", "barplot", "box", "image",
             "layout", "legend", "lines", "mtext", "par", "plot")
importFrom("stats", "cutree", "fisher.test", "p.adjust", "rgamma",
             "sd")
importFrom("utils", "capture.output", "combn", "packageVersion",
             "read.csv2", "read.table", "vignette", "write.csv2",
             "write.table")
importFrom("ape","read.nexus")
importFrom("ape","cophenetic.phylo")
importFrom("ape","subtrees")
#importFrom("Biostrings","consensusString")
#importFrom("Biostrings","readAAStringSet")
#importFrom("Biostrings","stringDist")
#importFrom("Biostrings","width")
#importFrom("Biostrings","subseq")
#importFrom("Biostrings","writeXStringSet")
#importFrom("Biostrings","AAStringSet")
