Given taxonomic information from a reference package and inter-node distances from a reference tree, perform classification of one or more placements provided by pplacer.
● Data Source:
BioConductor
● Keywords: classif
● Alias: classifyPlacements
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Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.
● Data Source:
BioConductor
● Keywords: classif, package
● Alias: clstutils, clstutils-package
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Outliers are defined as elements with edge length to the centermost element > cutoff. The distance threshold (cutoff) can be either specified, or calculated as a quantile of all pairwise distances in the matrix.
● Data Source:
BioConductor
● Keywords: classif
● Alias: findOutliers
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Given a square matrix of pairwise distances, return indices of N objects with a maximal sum of pairwise distances.
● Data Source:
BioConductor
● Keywords: classif
● Alias: maxDists
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Extends plot.phylo to draw a phylogenetic tree with additional annotation.
● Data Source:
BioConductor
● Keywords: aplot
● Alias: prettyTree
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Read the manifest file from a refpackage and return a list containing the package contents.
● Data Source:
BioConductor
● Keywords: classif
● Alias: refpkgContents
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Construct a data.frame providing the lineage of each sequence represented in the reference package.
● Data Source:
BioConductor
● Keywords: classif
● Alias: taxonomyFromRefpkg
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Provides objects (dists, paths) that can be used to calculate vectors of distances between an internal node and each leaf node. Also returns a square matrix of distances between leaf nodes.
● Data Source:
BioConductor
● Keywords: classif
● Alias: treeDists
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providing 
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