Man pages for heibl/megaptera
MEGAPhylogeny Techniques in R

addSingleTipAdd Tips to a Phylogenetic Tree
addTipsAdd Tips to a Phylogenetic Tree
BOLD2megapteraBarcode of Life Database Interface
cetaceaCetacea Phylogeny
checkBlocksSummarize and Plot Aligment Blocks
checkIdentityCoverageHistograms of Identity/Coverage per Locus
checkMissingSpecCheck for Missing Species
checkSpeciesGet Information about Species
checkSpecLocusBarplot of Species Numbers per Locus
checkSubsetCheck A Taxonomic Subset
collapseSinglesCollapse Singleton Edges
comprehensiveGuidetreeComprehensive Guide Tree
dbDNARead and Write DNA Sequences
dbManipulateSpecManipulate Single Species in Database
dbMaxGIPerSpecLimit Numbers of Sequences per Species
dbParsSet Database Parameters
dbPars-classClass "dbPars"
dbReadLocusTaxon-Locus-Crosstable
dbReadMSARead Sequences from Database
dbRenameSpeciesRename a Species
dbSummaryTaxonomyNumerical Summary of Taxonomy
dbTaxonomyRead and Write Taxonomy Table
dropExtendedIngroupExtract Ingroup Phylogeny from 'Extended Ingroup'
findInFlatfileFind Taxa and Accession Numbers in GenBank Flatfiles
findRootLineage Down to the Root
gbflat2dbRead GenBank Flatfiles
get3LetterCodeGenBank Division Code
higherTaxaOnEdgesHigher Taxa on Edges
icContingencyCumulative Contingency for Identity and Coverage
indet.stringsIdentify Undetermined Species
is.ingroupDoes a Taxon Belong to Ingroup?
locusLocus/Phylogenetic Marker Definition
locus-classClass "locus"
locusRef-classClass "locusRef"
megaptera2RmarkdownRMarkdown Report
megapteraInitInitialize MEGAPTERA
megaptera-internalInternal MEGAPTERA Functions
megaptera-packageMEGA-Phylogeny TEchniques in R
megapteraParsCreate an Object of Class "megapteraPars"
megapteraPars-classClass "megapteraPars"
megapteraProjBundle Input Data for the Pipeline
megapteraProj-classClass "megapteraProj"
ncbiGenomeFind Organelle Genomes on NCBI GenBank
ncbiTaxonomyNCBI Taxonomy Database
optimizeOptimal Coverage and Identity Thresholds
pdfPhyloA0Plot Large Phylogenies
pg2DNAbinConvert SQL Query Result to DNAbin
prune.phylo.rankPrune Phylogenies to Higher Ranks
selectMSASelection of Multiple Sequence Alignments
setLocusSet locus in megapteraProj
slicePhyloPlot Very Large Phylogenies
speclist2taxdumpUtilities for NCBI Taxdump
stepAStep A: Creating a Project Taxonomy
stepBStep B: Search and Download Sequences
stepBLASTstepBLASTN: Filter Homologous Sequences
stepBXStep BX: Add External Sequences
stepCStep C: Align Conspecific Sequences
stepDStep D: Calculate Benchmark Sequences
stepEStep E: Calculate Each Accession's Distance from Benchmark
stepFStep F: Select Sequences and Assemble FASTA file
stepGBLOCKSDetect Homology Uncertainty in Alingment
stepGenBankFTPExtract Records from GenBank Flatfiles
stepGUIDANCEDetect Homology Uncertainty in Alingment
stepHStep H: Detect and Separate Unalignable Blocks
stepMAFFTSTEP G: MAFFT Alignment
strip.infraspecTruncation of Species Names
strip.specExtract Genus Name from Linnean Binomial
supermatrixRetrieval and Concatentation of Multiple Sequence Alignments
surrogateTipsCongeneric Surrogate Species
taxdump2phyloUtilities for NCBI Taxdump
taxdumpAddNodeUtilities for NCBI Taxdump
taxdumpChangeParentUtilities for NCBI Taxdump
taxdumpChildrenUtilities for NCBI Taxdump
taxdumpDropTipUtilities for NCBI Taxdump
taxdumpHigherRankUtilities for NCBI Taxdump
taxdump_isTerminalUtilities for NCBI Taxdump
taxdumpLineageUtilities for NCBI Taxdump
taxdumpManageSynonymUtilities for NCBI Taxdump
taxdumpMRCAUtilities for NCBI Taxdump
taxdumpRankOrderUtilities for NCBI Taxdump
taxdumpSanitySanity Check for Parent-Child Taxonomic Tables
taxdumpSubsetUtilities for NCBI Taxdump
taxdumpSynonymUtilities for NCBI Taxdump
taxonDefinition of Species/Higher Taxa
taxon-classClass "taxon"
taxonGuidetree-classClass "taxonGuidetree"
heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.