clstutils: Tools for performing taxonomic assignment.

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Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.

Author
Noah Hoffman
Date of publication
None
Maintainer
Noah Hoffman <ngh2@uw.edu>
License
GPL-3
Version
1.22.0

View on Bioconductor

Man pages

classifyPlacements
Taxonomic classification by phylogenetic placement.
clstutils-package
Sequence based classification and selection of reference...
findOutliers
Identify outlier objects given a square distance matrix.
maxDists
Select a maximally diverse set of items given a distance...
prettyTree
Draw an annotated phylogenetic tree.
refpkgContents
Read the contents of a collection of reference sequences...
seqdat
Annotation for the Enterococcus sequence data set.
seqs
Enterococcus sequence data set.
taxonomyFromRefpkg
Extract taxonomic information from a refpkg.
treeDists
Provide objects for determining distances among nodes of a...

Files in this package

clstutils/DESCRIPTION
clstutils/NAMESPACE
clstutils/R
clstutils/R/placeTools.R
clstutils/R/prettyTree.R
clstutils/R/svgTree.R
clstutils/R/taxTools.R
clstutils/R/treeTools.R
clstutils/build
clstutils/build/vignette.rds
clstutils/data
clstutils/data/seqdat.rda
clstutils/data/seqs.rda
clstutils/devmakefile
clstutils/inst
clstutils/inst/doc
clstutils/inst/doc/pplacerDemo.R
clstutils/inst/doc/pplacerDemo.Rnw
clstutils/inst/doc/pplacerDemo.pdf
clstutils/inst/doc/refSet.R
clstutils/inst/doc/refSet.Rnw
clstutils/inst/doc/refSet.pdf
clstutils/inst/extdata
clstutils/inst/extdata/merged.distmat.bz2
clstutils/inst/extdata/merged.json
clstutils/inst/extdata/notes.txt
clstutils/inst/extdata/vaginal_16s.refpkg.tar.gz
clstutils/man
clstutils/man/classifyPlacements.Rd
clstutils/man/clstutils-package.Rd
clstutils/man/findOutliers.Rd
clstutils/man/maxDists.Rd
clstutils/man/prettyTree.Rd
clstutils/man/refpkgContents.Rd
clstutils/man/seqdat.Rd
clstutils/man/seqs.Rd
clstutils/man/taxonomyFromRefpkg.Rd
clstutils/man/treeDists.Rd
clstutils/tests
clstutils/tests/runalltests.R
clstutils/tests/runfile.sh
clstutils/tests/unit
clstutils/tests/unit/Makefile
clstutils/tests/unit/README.txt
clstutils/tests/unit/data_test.R
clstutils/tests/unit/dependencies_test.R
clstutils/tests/unit/placeTools_test.R
clstutils/tests/unit/setup.R
clstutils/tests/unit/taxTools_test.R
clstutils/tests/unit/treeTools_test.R
clstutils/vignettes
clstutils/vignettes/_makefile
clstutils/vignettes/pplacerDemo.Rnw
clstutils/vignettes/refSet.Rnw