Man pages for heibl/megaptera
MEGAPhylogeny Techniques in R
| addSingleTip | Add Tips to a Phylogenetic Tree |
| addTips | Add Tips to a Phylogenetic Tree |
| BOLD2megaptera | Barcode of Life Database Interface |
| cetacea | Cetacea Phylogeny |
| checkBlocks | Summarize and Plot Aligment Blocks |
| checkIdentityCoverage | Histograms of Identity/Coverage per Locus |
| checkMissingSpec | Check for Missing Species |
| checkSpecies | Get Information about Species |
| checkSpecLocus | Barplot of Species Numbers per Locus |
| checkSubset | Check A Taxonomic Subset |
| collapseSingles | Collapse Singleton Edges |
| comprehensiveGuidetree | Comprehensive Guide Tree |
| dbDNA | Read and Write DNA Sequences |
| dbManipulateSpec | Manipulate Single Species in Database |
| dbMaxGIPerSpec | Limit Numbers of Sequences per Species |
| dbPars | Set Database Parameters |
| dbPars-class | Class "dbPars" |
| dbReadLocus | Taxon-Locus-Crosstable |
| dbReadMSA | Read Sequences from Database |
| dbRenameSpecies | Rename a Species |
| dbSummaryTaxonomy | Numerical Summary of Taxonomy |
| dbTaxonomy | Read and Write Taxonomy Table |
| dropExtendedIngroup | Extract Ingroup Phylogeny from 'Extended Ingroup' |
| findInFlatfile | Find Taxa and Accession Numbers in GenBank Flatfiles |
| findRoot | Lineage Down to the Root |
| gbflat2db | Read GenBank Flatfiles |
| get3LetterCode | GenBank Division Code |
| higherTaxaOnEdges | Higher Taxa on Edges |
| icContingency | Cumulative Contingency for Identity and Coverage |
| indet.strings | Identify Undetermined Species |
| is.ingroup | Does a Taxon Belong to Ingroup? |
| locus | Locus/Phylogenetic Marker Definition |
| locus-class | Class "locus" |
| locusRef-class | Class "locusRef" |
| megaptera2Rmarkdown | RMarkdown Report |
| megapteraInit | Initialize MEGAPTERA |
| megaptera-internal | Internal MEGAPTERA Functions |
| megaptera-package | MEGA-Phylogeny TEchniques in R |
| megapteraPars | Create an Object of Class "megapteraPars" |
| megapteraPars-class | Class "megapteraPars" |
| megapteraProj | Bundle Input Data for the Pipeline |
| megapteraProj-class | Class "megapteraProj" |
| ncbiGenome | Find Organelle Genomes on NCBI GenBank |
| ncbiTaxonomy | NCBI Taxonomy Database |
| optimize | Optimal Coverage and Identity Thresholds |
| pdfPhyloA0 | Plot Large Phylogenies |
| pg2DNAbin | Convert SQL Query Result to DNAbin |
| prune.phylo.rank | Prune Phylogenies to Higher Ranks |
| selectMSA | Selection of Multiple Sequence Alignments |
| setLocus | Set locus in megapteraProj |
| slicePhylo | Plot Very Large Phylogenies |
| speclist2taxdump | Utilities for NCBI Taxdump |
| stepA | Step A: Creating a Project Taxonomy |
| stepB | Step B: Search and Download Sequences |
| stepBLAST | stepBLASTN: Filter Homologous Sequences |
| stepBX | Step BX: Add External 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 |
| stepGBLOCKS | Detect Homology Uncertainty in Alingment |
| stepGenBankFTP | Extract Records from GenBank Flatfiles |
| stepGUIDANCE | Detect Homology Uncertainty in Alingment |
| stepH | Step H: Detect and Separate Unalignable Blocks |
| stepMAFFT | STEP G: MAFFT Alignment |
| strip.infraspec | Truncation of Species Names |
| strip.spec | Extract Genus Name from Linnean Binomial |
| supermatrix | Retrieval and Concatentation of Multiple Sequence Alignments |
| surrogateTips | Congeneric Surrogate Species |
| taxdump2phylo | Utilities for NCBI Taxdump |
| taxdumpAddNode | Utilities for NCBI Taxdump |
| taxdumpChangeParent | Utilities for NCBI Taxdump |
| taxdumpChildren | Utilities for NCBI Taxdump |
| taxdumpDropTip | Utilities for NCBI Taxdump |
| taxdumpHigherRank | Utilities for NCBI Taxdump |
| taxdump_isTerminal | Utilities for NCBI Taxdump |
| taxdumpLineage | Utilities for NCBI Taxdump |
| taxdumpManageSynonym | Utilities for NCBI Taxdump |
| taxdumpMRCA | Utilities for NCBI Taxdump |
| taxdumpRankOrder | Utilities for NCBI Taxdump |
| taxdumpSanity | Sanity Check for Parent-Child Taxonomic Tables |
| taxdumpSubset | Utilities for NCBI Taxdump |
| taxdumpSynonym | Utilities for NCBI Taxdump |
| taxon | Definition of Species/Higher Taxa |
| taxon-class | Class "taxon" |
| taxonGuidetree-class | Class "taxonGuidetree" |
