Man pages for bomeara/sleq
sleq
| cbind.seqalignment | Combines seqalignment objects and drops duplicate taxa |
| CleanSeqs | Removes sites that contain a certain percentage of missing... |
| ConvertNCBINodesToTree | From an NCBI taxonomy download, return a tree in igraphy... |
| CountIdenticalSeqs | Calculate number of identical sequences |
| CreateBirdsEyeView | Create a birds' eye view of the data |
| DeleteIdenticalSeqs | Delete identical sequences |
| dim.seqalignment | Override dim() for a seqalignment object to get dim of the... |
| DownloadNCBITaxonomy | Download the taxonomy from NCBI |
| GetCodonPhase | Determine the best codon phase and return amino acid sequence |
| GetDescendantIDs | Go from an NCBI id to the ids of its descendants (all the... |
| GetDescendantNamesFromName | Go from a taxon name to the names of all its descendants |
| GetIDFromName | Convert from a taxon name to its NCBI id |
| GetNameFromID | Convert from an NCBI id to a taxon name |
| GetNCBITaxa | Create a data.frame with NCBI taxon id, name, and what kind... |
| GetSequenceType | Get the type of a alignment |
| names.seqalignment | Override names() for seqaligment object |
| PurgeBadSites | Removes poorly aligned sequences using a sliding window |
| seqalignment | Create seqalignment class object |
| SeqLengthNoGaps | Provides length a sequence for each taxon in an alignment... |
| SingleTaxonCompare | Function that will summarize variability by site comparing... |
| SiteMissing | Get the proportion of non-ambiguous data across each site |
| sleq | Utilities for dealing with sequence data in R |
| sub-.seqalignment | Using the bracket operator to go into the sequences inside a... |
| subset.seqalignment | Get a subset of a seqalignment object, returning another... |
| TossTaxa | Toss taxa (rows) for which coverage across all genes is below... |
