Man pages for megaptera
MEGAPhylogeny Techniques in R
| 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" |
