seaview: SeaView: DNA sequences and phylogenetic tree viewer

In bioseq: A Toolbox for Manipulating Biological Sequences

SeaView: DNA sequences and phylogenetic tree viewer

Description

This function opens SeaView (Gouy, Guindon & Gascuel, 2010) to visualize biological sequences and phylogenetic trees. The software must be installed on the computer.

Usage

seaview(
  x,
  seaview_exec = getOption("bioseq.seaview.exec", default = "seawiew")
)

Arguments

x	a DNA, RNA or AA vector. Alternatively a DNAbin or AAbin object or a phylogenetic tree (class phylo).
seaview_exec	a character string giving the path of the program.

Details

By default, the function assumes that the executable is installed in a directory located on the PATH. Alternatively the user can provide an absolute path to the executable (i.e. the location where the software was installed/uncompressed). This can be stored in the global options settings using options(bioseq.seaview.exec = "my_path_to_seaview").

References

Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224.

See Also

Other GUI wrappers: aliview()

bioseq documentation built on Sept. 6, 2022, 5:07 p.m.