megaptera: MEGAPhylogeny Techniques in R
Version 1.0-0

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

Browse man pages Browse package API and functions Browse package files

AuthorChristoph Heibl
Date of publication2014-11-13 08:44:56
MaintainerChristoph Heibl <christoph.heibl@gmx.net>
LicenseGPL (>= 2)
Version1.0-0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("megaptera")

Man pages

addTip: Add Tips to a Phylogeny
cetacea: Cetacea Phylogeny
check.Function: Check SUSILI Results
dbPars: Set Database Parameters
dbPars-class: Class "dbPars"
dbReadTaxonomy: Taxonomy of Species Contained in SQL Database
dbUpdateTaxonomy: Taxonomy Table
fleshoutGuidetree: Add Missing Species to a Phylogenetic Tree
io.dna.db: Read and Write DNA Sequences from/to PgSQL Database
locus: Locus/Phylogenetic Marker Definition
locus-class: Class "locus"
megaptera-internal: Internal MEGAPTERA Functions
megaptera-package: MEGAPhylogenie TEchniques in R
megapteraPars: Set Pipeline Parameters
megapteraPars-class: Class "megapteraPars"
megapteraProj: Bundle Input Data for the Pipeline
megapteraProj-class: Class "megapteraProj"
NCBIeaa: NCBI Extended Amino Acid
ncbiTaxonomy: NCBI Taxonomy Database
prune.phylo.rank: Prune Phylogenies
setLocus: Set locus in megapteraProj
stepA: Step A: Download a NCBI Taxonomy
stepB: Step B: Search and Download Sequences
stepC: Step C: Align Conspecific Sequences
stepD: Step D: Calculate Benchmark Sequences
stepE: Step E: Calculate Each Accession's Distance from Benchmark
stepF: Step F: Select Sequences and Assemble FASTA file
stepG: Step G: Profile Alignment
stepH: Step H: Detect and Separate Unalignable Blocks
strip.infraspec: Truncation of Species Names
taxon: Definition of Species/Higher Taxa
taxon-class: Class "taxon"

Functions

EFetchHigherTaxon Man page
EFetchLocus Man page
MAD Man page
NCBI.wrap Man page
NCBIeaa Man page
addNbAcc Man page
addTip Man page
alignGenus Man page
calcDistToRef Man page
cetacea Man page
check.Clades Man page
check.Coverage Man page
check.Markers Man page
check.NameChanges Man page
check.Species Man page
check.TaxAgainstPhy Man page
compare.phylo.backbone Man page
conn Man page
coverage Man page
dbAutoFillTaxonomy Man page
dbDeleteSpec Man page
dbPars Man page
dbPars-class Man page
dbReadDNA Man page
dbReadDNAbin Man page
dbReadReference Man page
dbReadTaxonomy Man page
dbUpdateLocus Man page
dbUpdateTaxonomy Man page
dbWriteDNA Man page
dbWriteDNAbin Man page
dbWriteString Man page
dbconnect Man page
downloadSequences Man page
esearch Man page
extractLocus Man page
filter.alignment Man page
fixTaxonomy Man page
fleshoutGuidetree Man page
force.mp Man page
funX Man page
getGeneRange Man page
getLineage Man page
getMaxDist Man page
insert.tip.phylo Man page
is.alignable Man page
loci Man page
locus Man page
locus-class Man page
mafft.merge Man page
markersGenbank Man page
maxDist Man page
maxDistMPI Man page
meanPairwiseIdentity Man page
megaptera-package Man page
megapteraHeatmap Man page
megapteraPars Man page
megapteraPars-class Man page
megapteraProj Man page
megapteraProj-class Man page
myDist Man page
ncbiLineage Man page
ncbiTaxonomy Man page
nucleotideOverlap Man page
pars Man page
prune.phylo.rank Man page
read.benchmark.db Man page
revCompTest Man page
select.seqs Man page
setLocus Man page
slog Man page
sortRanks Man page
specCons Man page
speciesConsensus Man page
splitGiTaxon Man page
sql.conform Man page
sql.wrap Man page
sqlTaxonomyHeader Man page
stepA Man page
stepAA Man page
stepB Man page
stepC Man page
stepD Man page
stepE Man page
stepF Man page
stepG Man page
stepH Man page
strip.infraspec Man page
strip.spec Man page
summary.sproj Man page
supermatrix Man page
tab Man page
tax Man page
tax2tree Man page
taxon Man page
taxon-class Man page
term Man page
unalignable Man page
whereToInsert Man page
write.dna.spectable Man page

Files

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
megaptera documentation built on Jan. 15, 2017, 11:19 p.m.