
export(SelacOptimize, SelonOptimize, SelacSimulator, SelonSimulator, NucSimulator, SelacSimulatorEvolvingRates, GetFunctionality, GetSelacSiteLikelihoods, GetPartitionOrder, GetMarginalAllGenes, GetAdequateSelac, GetAdequateManyReps)
import(ape, deSolve, nloptr, nnet, data.table, phangorn)
importFrom(seqinr, a, aaa, AAstat, acnucopen, al2bp, alllistranks, amb, as.matrix.alignment, autosocket, baselineabif, bma, c2s, cai, choosebank, circle, closebank, col2alpha, comp, computePI, count, countfreelists, countsubseqs, crelistfromclientdata, dia.bactgensize, dist.alignment, dotchart.uco, dotPlot, draw.oriloc, draw.rearranged.oriloc, draw.recstat, extract.breakpoints, extractseqs, fastacc, gb2fasta, gbk2g2, gbk2g2.euk, get.db.growth, get.ncbi, getAnnot, getFrag, getKeyword, getLength, getlistrank, getliststate, getLocation, getName, getSequence, getTrans, getType, gfrag, ghelp, isenum, kaks, knowndbs, lseqinr, modifylist, move, n2s, oriloc, parser.socket, peakabif, permutation, plot.SeqAcnucWeb, plotabif, plotladder, plotPanels, pmw, prepgetannots, prettyseq, print.qaw, print.SeqAcnucWeb, query, read.abif, read.alignment, read.fasta, readBins, readfirstrec, readPanels, readsmj, rearranged.oriloc, recstat, residuecount, reverse.align, rot13, s2c, s2n, savelist, setlistname, splitseq, stresc, stutterabif, swap, syncodons, synsequence, tablecode, test.co.recstat, test.li.recstat, translate, trimSpace, uco, ucoweight, where.is.this.acc, words, words.pos, write.fasta)
importFrom(expm, expm, "%^%")
importFrom("methods", "is")
importFrom(MASS, Null)
importFrom(parallel, mclapply)
importFrom(GenSA, GenSA)
S3method(print, selac)
S3method(print, selon)
importFrom("graphics", "abline", "axis", "par", "plot", "symbols")
importFrom("stats", "dist", "pgamma", "qgamma", "quantile", "reorder",
           "rnorm", "runif", "optimize", "weighted.mean")
importFrom("utils", "read.delim")
importFrom("RColorBrewer", "brewer.pal")
importFrom("grDevices", "col2rgb", "rgb")
importFrom("graphics", "legend", "lines", "points")
importFrom("stats", "median")
importFrom("stats", "rgamma")
importFrom(statmod, gauss.quad.prob)
