Man pages for olli0601/phyloscan
| cmd.iqtree | Produce a single iqtree shell command. |
| phsc.bam.get.length.and.pos.of.mergedreads | Calculate position and length of merged reads |
| phsc.cmd.bam.calculate.read.distribution | Generate bash commands to calculate read distribution in bam... |
| phsc.cmd.phyloscanner.multi | Generate bash commands for multiple phyloscanner runs |
| phsc.cmd.phyloscanner.one | Generate bash command for a single phyloscanner run |
| phsc.cmd.phyloscanner.one.resume | Generate bash command to resume a single phyloscanner run |
| phsc.cmd.phyloscanner.one.resume.combinewindows | Generate bash command to combine single window resumes of a... |
| phsc.cmd.phyloscanner.one.resume.onewindow | Generate bash command to resume a single window of a... |
| phsc.cmd.process.phyloscanner.output.in.directory | Generate bash commands to process phyloscanner output |
| phsc.define.stage1.analyses | Determine stage 1 phyloscanner runs |
| phsc.find.bam.and.references | Find bam and corresponding reference files |
| phsc.find.linked.pairs | Find pairs of individuals between whom linkage is not... |
| phsc.find.transmission.networks.from.linked.pairs | Find phylogenetic transmission networks |
| phsc.get.assignments.by.window.for.couple | Get transmission assignments per window |
| phsc.get.basic.pairwise.relationships | Calculate basic pairwise relationships |
| phsc.get.most.likely.transmission.chains | Reconstruct most likely transmission chains |
| phsc.get.most.likely.transmission.chains.greedy | Reconstruct most likely transmission chains, greedy algorithm |
| phsc.get.most.likely.transmission.chains.RBGLedmonds | Construct maximum probability transmission network |
| phsc.get.pairwise.relationships | Calculate pairwise relationships |
| phsc.get.pairwise.relationships.keff.and.neff | Count observed relationship states |
| phsc.get.pairwise.relationships.likelihoods | Wrapper script to calculate pairwise relationships and... |
| phsc.get.pairwise.relationships.posterior | Calculate marginal posterior probability for two individuals... |
| phsc.get.prior.parameter.n0 | Calculate prior parameter n0 |
| phsc.plot.default.colours.for.relationtypes | Default colours for relationship types |
| phsc.plot.maxedge.network | Plot probability network with most likely edges |
| phsc.plot.most.likely.transmission.chain | Plot most likely transmission chain |
| phsc.plot.phycollapsed.selected.individuals | Plot short read phylogenies and highlight individuals |
| phsc.plot.phyloscan | Plot phyloscan |
| phsc.plot.phy.selected.individuals | Plot short read phylogenies and highlight individuals |
| phsc.plot.phy.selected.pairs | Plot all short read phylogenies including two individuals |
| phsc.plot.transmission.network | Plot transmission network |
| phsc.plot.windowassignments.by.runs | Compare window assignments by different phyloscanner runs |
| phsc.plot.windowsummaries.for.pairs | Plot window summaries for pairs of individuals |
| phsc.read.likelytransmissions | Read likely transmissions summary files into a data.table |
| phsc.read.processed.phyloscanner.output.in.directory | Read processed phyloscanner output |
| phsc.read.subtrees | Read subtree information |
| phsc.read.trees | Read short read trees |
| raxml.cmd | Generate bash commands to generate phylogenies with RAxML |
