Man pages for megaptera
MEGAPhylogeny Techniques in R

addTipAdd Tips to a Phylogeny
cetaceaCetacea Phylogeny
check.FunctionCheck SUSILI Results
dbParsSet Database Parameters
dbPars-classClass "dbPars"
dbReadTaxonomyTaxonomy of Species Contained in SQL Database
dbUpdateTaxonomyTaxonomy Table
fleshoutGuidetreeAdd Missing Species to a Phylogenetic Tree
io.dna.dbRead and Write DNA Sequences from/to PgSQL Database
locusLocus/Phylogenetic Marker Definition
locus-classClass "locus"
megaptera-internalInternal MEGAPTERA Functions
megaptera-packageMEGAPhylogenie TEchniques in R
megapteraParsSet Pipeline Parameters
megapteraPars-classClass "megapteraPars"
megapteraProjBundle Input Data for the Pipeline
megapteraProj-classClass "megapteraProj"
NCBIeaaNCBI Extended Amino Acid
ncbiTaxonomyNCBI Taxonomy Database
prune.phylo.rankPrune Phylogenies
setLocusSet locus in megapteraProj
stepAStep A: Download a NCBI Taxonomy
stepBStep B: Search and Download 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
stepGStep G: Profile Alignment
stepHStep H: Detect and Separate Unalignable Blocks
strip.infraspecTruncation of Species Names
taxonDefinition of Species/Higher Taxa
taxon-classClass "taxon"
megaptera documentation built on Jan. 15, 2017, 11:19 p.m.