NCBIeaa                 NCBI Extended Amino Acid
addTip                  Add Tips to a Phylogeny
cetacea                 Cetacea Phylogeny
check.Clades            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
fleshoutGuidetree       Add Missing Species to a Phylogenetic Tree
locus                   Locus/Phylogenetic Marker Definition
locus-class             Class "locus"
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"
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"
