Global functions | |
---|---|
.onAttach | Source code |
.onLoad | Source code |
cmd.hpcwrapper.cx1.ic.ac.uk | Source code |
cmd.iqtree | Man page 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.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 |
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 |
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