| .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
|
