All functions
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phsc.bam.get.length.and.pos.of.mergedreads()
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Calculate position and length of merged reads |
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phsc.cmd.bam.calculate.read.distribution()
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Generate bash commands to calculate read distribution in bam file |
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phsc.cmd.phyloscanner.multi()
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Generate bash commands for multiple phyloscanner runs |
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phsc.cmd.phyloscanner.one()
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Generate bash command for a single phyloscanner run |
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phsc.cmd.phyloscanner.one.resume()
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Generate bash command to resume a single phyloscanner run |
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phsc.define.stage1.analyses()
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Determine stage 1 phyloscanner runs |
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phsc.find.bam.and.references()
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Find bam and corresponding reference files |
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phsc.find.linked.pairs()
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Find pairs of individuals between whom linkage is not excluded phylogenetically |
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phsc.find.transmission.networks.from.linked.pairs()
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Find phylogenetic transmission networks |
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phsc.plot.most.likely.transmission.chain()
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Plot most likely transmission chain |
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phsc.plot.phy.selected.individuals()
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Plot short read phylogenies and highlight individuals |
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phsc.plot.phy.selected.pairs()
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Plot all short read phylogenies including two individuals |
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phsc.plot.phycollapsed.selected.individuals()
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Plot short read phylogenies and highlight individuals |
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phsc.plot.phyloscan()
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Plot phyloscan |
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phsc.plot.transmission.network()
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Plot transmission network |
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raxml.cmd()
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Generate bash commands to generate phylogenies with RAxML |