rfamSeedTree: Get the phylogenetic tree of the seed multiple alignment of...

In LaraSellesVidal/rfaRm: An R interface to the Rfam database

Description

Gets the phylogenetic tree of the seed multiple alignment associated to the Rfam family. The tree is retrieved in the NHX format (New Hampshire extended format. The tree will be saved to the path specified through filename. The generated file can be read directly with the treeio R package.

Usage

rfamSeedTree(rfamFamily, filename)

Arguments

rfamFamily	string with an Rfam family accession or ID for which the phylogenetic tree of the seed alignment should be retrieved.
filename	string indicating a path to which the phylogenetic tree in the NHX format should be written.

Value

A string with the phylogenetic tree of the seed alignment of the Rfam family in the NHX format. The tree will also be written to the specified path, producing a file that can be read by the treeio package.

References

Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, Anton I Petrov, Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D335–D342, https://doi.org/10.1093/nar/gkx1038

https://docs.rfam.org/en/latest/api.html

Examples

# Retrieve the phylogenetic tree of the seed alignment for the Rfam family with
# ID "FMN" and save it to a file

rfamSeedTree("FMN", filename="FMNseedTree.nhx")

# Retrieve the phylogenetic tree of the seed alignment for the Rfam family with
# accession "RF00174" and save it to a file

rfamSeedTree("RF00174", filename="RF00174seedTree.nhx")

LaraSellesVidal/rfaRm documentation built on Aug. 8, 2021, 7:25 p.m.