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msaplot

msaplot

Description

multiple sequence alignment with phylogenetic tree

Usage

msaplot(
  p,
  fasta,
  offset = 0,
  width = 1,
  color = NULL,
  window = NULL,
  bg_line = TRUE,
  height = 0.8
)

Arguments

p

tree view
fasta

fasta file, multiple sequence alignment
offset

offset of MSA to tree
width

total width of alignment, compare to width of tree
color

color
window

specific a slice to display
bg_line

whether add background line in alignment
height

height ratio of sequence

Value

tree view

Author(s)

Guangchuang Yu

ggtree

an R package for visualization of tree and annotation data

v2.4.2
Artistic-2.0
Authors
Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut] (<https://orcid.org/0000-0003-3513-5362>), Yonghe Xia [ctb], Justin Silverman [ctb], Bradley Jones [ctb], Watal M. Iwasaki [ctb], Ruizhu Huang [ctb]
Initial release

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