API for olli0601/phyloscan

Global functions
onAttach Source code
onLoad Source code
phsc.bam.get.length.and.pos.of.mergedreads Man page Source code
phsc.cmd.LikelyTransmissions Source code
phsc.cmd.LikelyTransmissionsSummary Source code
phsc.cmd.NormalisationLookupWriter Source code
phsc.cmd.SplitPatientsToSubGraphs Source code
phsc.cmd.SplitPatientsToSubtrees Source code
phsc.cmd.SummaryStatistics Source code
phsc.cmd.bam.calculate.read.distribution Man page Source code
phsc.cmd.blacklist.downsample Source code
phsc.cmd.blacklist.dualinfections Source code
phsc.cmd.blacklist.parsimonybased Source code
phsc.cmd.blacklist.reads Source code
phsc.cmd.blacklist.rogue.extremeprob Source code
phsc.cmd.blacklist.rogue.geneticdistance Source code
phsc.cmd.mafft.add Source code
phsc.cmd.pairwise.relationships Source code
phsc.cmd.phyloscanner.multi Man page Source code
phsc.cmd.phyloscanner.one Man page Source code
phsc.cmd.phyloscanner.one.resume Man page Source code
phsc.cmd.phyloscanner.one.resume.combinewindows Man page Source code
phsc.cmd.phyloscanner.one.resume.onewindow Man page Source code
phsc.cmd.process.phyloscanner.output.in.directory Man page Source code
phsc.cmd.read.processed.phyloscanner.output.in.directory Source code
phsc.define.stage1.analyses Man page Source code
phsc.drop.tip Source code
phsc.extract.clade Source code
phsc.find.bam.and.references Man page Source code
phsc.find.linked.pairs Man page Source code
phsc.find.transmission.networks.from.linked.pairs Man page Source code
phsc.get.assignments.by.window.for.couple Man page Source code
phsc.get.basic.pairwise.relationships Man page Source code
phsc.get.most.likely.transmission.chains Man page Source code
phsc.get.most.likely.transmission.chains.RBGLedmonds Man page Source code
phsc.get.most.likely.transmission.chains.greedy Man page Source code
phsc.get.pairwise.relationships Man page Source code
phsc.get.pairwise.relationships.keff.and.neff Man page Source code
phsc.get.pairwise.relationships.likelihoods Man page Source code
phsc.get.pairwise.relationships.numbers Source code
phsc.get.pairwise.relationships.posterior Man page Source code
phsc.get.prior.parameter.n0 Man page Source code
phsc.phy.collapse.monophyletic.clades Source code
phsc.plot.default.colours.for.relationtypes Man page Source code
phsc.plot.maxedge.network Man page Source code
phsc.plot.most.likely.transmission.chain Man page Source code
phsc.plot.phy.selected.individuals Man page Source code
phsc.plot.phy.selected.pairs Man page Source code
phsc.plot.phycollapsed.selected.individuals Man page Source code
phsc.plot.phyloscan Man page Source code
phsc.plot.transmission.network Man page Source code
phsc.plot.windowassignments.by.runs Man page Source code
phsc.plot.windowsummaries.for.pairs Man page Source code
phsc.read.likelytransmissions Man page Source code
phsc.read.processed.phyloscanner.output.in.directory Man page Source code
phsc.read.subtrees Man page Source code
phsc.read.trees Man page Source code
raxml.cmd Man page Source code
simplify.summary Source code
olli0601/phyloscan documentation built on Nov. 9, 2018, 10:03 a.m.