NAMESPACE

# Generated by roxygen2: do not edit by hand

export(cmd.examl)
export(cmd.examl.bootstrap)
export(cmd.examl.bootstrap.on.one.machine)
export(cmd.examl.bsalignment)
export(cmd.examl.bsstarttree)
export(cmd.examl.cleanup)
export(cmd.examl.single)
export(cmd.fasttree)
export(cmd.fasttree.add.bootstrap.nodelabels.to.base.tree)
export(cmd.fasttree.many.bootstraps)
export(cmd.fasttree.one.bootstrap)
export(cmd.hpccaller)
export(cmd.hpcwrapper.cx1.ic.ac.uk)
export(cmd.jmodeltest)
export(cmd.lsd)
export(cmd.lsd.dates)
export(cmd.multi2di)
export(cmd.mvr)
export(cmd.phydstar)
export(cmd.raxml)
export(cmd.rm.resistance)
export(cmd.strip.gaps)
export(cmd.treedater)
export(cmd.treedater.script)
export(pipeline.ExaML.bootstrap.per.proc)
export(prog.examl.getbootstrapseq)
export(seq.align.based.on.common.reference)
export(seq.blast)
export(seq.blast.read)
export(seq.create.referencepairs)
export(seq.dist)
export(seq.find)
export(seq.gc.content)
export(seq.length)
export(seq.mvr.d.and.v)
export(seq.proportion.ambiguous)
export(seq.read.GenBank)
export(seq.replace)
export(seq.rm.drugresistance)
export(seq.rmgaps)
export(seq.strip.gap)
export(seq.unique)
export(seq.write.dna.nexus)
export(seq.write.dna.phylip)
export(seq.write.dna.phylip.triangular)
import(ape)
import(data.table)
import(ggplot2)
import(plyr)
import(treedater)