MEGAPhylogeny Techniques in R


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Documentation for package ‘megaptera’ version 1.0-0

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megaptera-package MEGAPhylogenie TEchniques in R
addTip Add Tips to a Phylogeny
cetacea Cetacea Phylogeny
check.Clades Check SUSILI Results
check.Coverage Check SUSILI Results
check.Markers Check SUSILI Results
check.NameChanges Check SUSILI Results
check.Species Check SUSILI Results
dbPars Set Database Parameters
dbPars-class Class "dbPars"
dbReadDNA Read and Write DNA Sequences from/to PgSQL Database
dbReadTaxonomy Taxonomy of Species Contained in SQL Database
dbUpdateTaxonomy Taxonomy Table
dbWriteDNA Read and Write DNA Sequences from/to PgSQL Database
fleshoutGuidetree Add Missing Species to a Phylogenetic Tree
locus Locus/Phylogenetic Marker Definition
locus-class Class "locus"
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
strip.spec Truncation of Species Names
taxon Definition of Species/Higher Taxa
taxon-class Class "taxon"