List number of available genomes in each taxonomic group

Users can retrieve the available number of sequenced genomes per group. Only available for db = "refseq" and db = "genbank".

Usage

listGroups(db = "refseq", kingdom = "all", details = FALSE)

Arguments

db

a character string specifying the database for which genome availability shall be checked. Available options are:

• db = "refseq"

• db = "genbank"

kingdom

a kingdom specification retrieved by getKingdoms.

details

shall all species corresponding to the specified kingdom be returned? Default is details = FALSE.

See also

listGenomes, is.genome.available, listKingdoms

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# example for refseq
listGroups(db = "refseq")
# example for genbank
listGroups(db = "genbank")
### in case groups should be specified by kingdom
# first, retrieve available kingdom names
listKingdoms()
# now we choose kingdom "bacteria"
listGroups(db = "refseq", kingdom = "bacteria")
# or
listGroups(db = "genbank", kingdom = "bacteria")
}