megaptera: MEGAPhylogeny Techniques in R

Given a set of taxa and marker, the goal is build a complete and correct sequence alignment for phylogenetic analysis.

AuthorChristoph Heibl
Date of publication2014-11-13 08:44:56
MaintainerChristoph Heibl <christoph.heibl@gmx.net>
LicenseGPL (>= 2)
Version1.0-0

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Files in this package

megaptera
megaptera/inst
megaptera/inst/doc
megaptera/inst/doc/Getting-started.rnw
megaptera/inst/doc/Getting-started.pdf
megaptera/NAMESPACE
megaptera/data
megaptera/data/input.rda
megaptera/data/NCBIeaa.rda
megaptera/data/cetacea.rda
megaptera/R
megaptera/R/sql.wrap.R megaptera/R/dbWriteDNA.R megaptera/R/fleshoutGuidetree.R megaptera/R/ncbiLineage.R megaptera/R/revCompTest.R megaptera/R/locus.R megaptera/R/EFetchLocus.R megaptera/R/filter.alignment.R megaptera/R/stepC.R megaptera/R/megapteraProj.R megaptera/R/dbUpdateTaxonomy.R megaptera/R/check.Species.R megaptera/R/tax2tree.R megaptera/R/check.TaxAgainstPhy.R megaptera/R/sqlTaxonomyHeader.R megaptera/R/strip.infraspec.R megaptera/R/myDist.R megaptera/R/dbReadDNA.R megaptera/R/write.dna.spectable.R megaptera/R/splitGiTaxon.R megaptera/R/supermatrix.R megaptera/R/speciesConsensus.R megaptera/R/stepG.R megaptera/R/markersGenbank.R megaptera/R/strip.spec.R megaptera/R/sql.conform.R megaptera/R/prune.phylo.rank.R megaptera/R/stepH.R megaptera/R/slog.R megaptera/R/addTip.R megaptera/R/dbUpdateLocus.R megaptera/R/stepA.R megaptera/R/getLineage.R megaptera/R/meanPairwiseIdentity.R megaptera/R/check.NameChanges.R megaptera/R/dbDeleteSpec.R megaptera/R/calcDistToRef.R megaptera/R/specCons.R megaptera/R/term.R megaptera/R/coverage.R megaptera/R/MAD.R megaptera/R/funX.R megaptera/R/extractLocus.R megaptera/R/megaptera_heatmap.R megaptera/R/check.Markers.R megaptera/R/sortRanks.R megaptera/R/stepF.R megaptera/R/stepE.R megaptera/R/is.alignable.R
megaptera/R/dbWriteString.r
megaptera/R/alignGenus.R megaptera/R/mafft.merge.R megaptera/R/whereToInsert.R megaptera/R/downloadSequences.R megaptera/R/dbAutofillTaxonomy.R megaptera/R/check.Clades.R megaptera/R/addNbAcc.R megaptera/R/NCBI.wrap.R megaptera/R/esearch.R megaptera/R/dbReadTaxomony.R megaptera/R/taxon.R megaptera/R/check.Coverage.R megaptera/R/nucleotideOverlap.R megaptera/R/dbPars.R megaptera/R/stepD.R megaptera/R/dbReadReference.R megaptera/R/maxDist.R megaptera/R/fixTaxonomy.R megaptera/R/megapteraPars.R megaptera/R/ncbiTaxonomy.R megaptera/R/stepB.R
megaptera/vignettes
megaptera/vignettes/Getting-started-concordance.tex
megaptera/vignettes/Getting-started.rnw
megaptera/vignettes/jbiogeo2.bst
megaptera/vignettes/biology.bib
megaptera/MD5
megaptera/build
megaptera/build/vignette.rds
megaptera/DESCRIPTION
megaptera/man
megaptera/man/megaptera-internal.Rd megaptera/man/dbPars.Rd megaptera/man/stepE.Rd megaptera/man/addTip.Rd megaptera/man/check.Function.Rd megaptera/man/strip.infraspec.Rd megaptera/man/prune.phylo.rank.Rd megaptera/man/megapteraPars.Rd megaptera/man/locus-class.Rd megaptera/man/io.dna.db.Rd megaptera/man/taxon-class.Rd megaptera/man/megapteraPars-class.Rd megaptera/man/stepA.Rd megaptera/man/dbReadTaxonomy.Rd megaptera/man/stepC.Rd megaptera/man/megapteraProj.Rd megaptera/man/stepG.Rd megaptera/man/stepB.Rd megaptera/man/megaptera-package.Rd megaptera/man/dbPars-class.Rd megaptera/man/ncbiTaxonomy.Rd megaptera/man/fleshoutGuidetree.Rd megaptera/man/taxon.Rd megaptera/man/stepF.Rd megaptera/man/locus.Rd megaptera/man/cetacea.Rd megaptera/man/stepD.Rd megaptera/man/NCBIeaa.Rd megaptera/man/dbUpdateTaxonomy.Rd megaptera/man/stepH.Rd megaptera/man/megapteraProj-class.Rd megaptera/man/setLocus.Rd

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