Man pages for bomeara/sleq
sleq

cbind.seqalignmentCombines seqalignment objects and drops duplicate taxa
CleanSeqsRemoves sites that contain a certain percentage of missing...
ConvertNCBINodesToTreeFrom an NCBI taxonomy download, return a tree in igraphy...
CountIdenticalSeqsCalculate number of identical sequences
CreateBirdsEyeViewCreate a birds' eye view of the data
DeleteIdenticalSeqsDelete identical sequences
dim.seqalignmentOverride dim() for a seqalignment object to get dim of the...
DownloadNCBITaxonomyDownload the taxonomy from NCBI
GetCodonPhaseDetermine the best codon phase and return amino acid sequence
GetDescendantIDsGo from an NCBI id to the ids of its descendants (all the...
GetDescendantNamesFromNameGo from a taxon name to the names of all its descendants
GetIDFromNameConvert from a taxon name to its NCBI id
GetNameFromIDConvert from an NCBI id to a taxon name
GetNCBITaxaCreate a data.frame with NCBI taxon id, name, and what kind...
GetSequenceTypeGet the type of a alignment
names.seqalignmentOverride names() for seqaligment object
PurgeBadSitesRemoves poorly aligned sequences using a sliding window
seqalignmentCreate seqalignment class object
SeqLengthNoGapsProvides length a sequence for each taxon in an alignment...
SingleTaxonCompareFunction that will summarize variability by site comparing...
SiteMissingGet the proportion of non-ambiguous data across each site
sleqUtilities for dealing with sequence data in R
sub-.seqalignmentUsing the bracket operator to go into the sequences inside a...
subset.seqalignmentGet a subset of a seqalignment object, returning another...
TossTaxaToss taxa (rows) for which coverage across all genes is below...
bomeara/sleq documentation built on Feb. 24, 2018, 7:53 p.m.