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msaviewr

Interactive multiple sequence alignment viewer for R, powered by react-msaview. Renders as an htmlwidget in RStudio, R Markdown, Quarto, and Shiny.

MSA Viewer screenshot

Installation

# Install from the local package
devtools::install("packages/r-msaview")

# Or install dependencies and load directly
install.packages("htmlwidgets")

For Bioconductor interop:

BiocManager::install(c("Biostrings", "ggtree", "treeio"))

Quick start

library(msaviewr)

msaview(
  msa = ">human\nMVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH\n>mouse\nMVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSH\n>goat\nMSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHS",
  tree = "((human:0.1,mouse:0.2):0.05,goat:0.3);"
)

Examples

Named character vector

seqs <- c(
  human = "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH",
  mouse = "MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSH",
  goat  = "MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHS"
)
msaview(msa = seqs, tree = "((human:0.1,mouse:0.2):0.05,goat:0.3);")

From files

msaview(msa = "alignment.stock")
msaview(msa = "alignment.fa", tree = "tree.nwk")

With ape

library(ape)

tree <- rtree(15)
seqs <- setNames(
  replicate(15, paste0(sample(c("A","C","G","T"), 300, TRUE), collapse = "")),
  tree$tip.label
)
msaview(msa = seqs, tree = tree, color_scheme = "nucleotide")

Cladogram (no branch lengths)

msaview(msa = seqs, tree = tree, show_branch_len = FALSE)

With Biostrings

library(Biostrings)

# DNAStringSet
dna <- DNAStringSet(c(
  seq1 = "ATGCGATCGATCGATCG--ATCG",
  seq2 = "ATGCGATCGATCGATCGATCGATCG",
  seq3 = "ATGCG--CGATCGATCGATCGATCG",
  seq4 = "ATGCGATCGATCGATCG--ATCG"
))
msaview(msa = dna, color_scheme = "nucleotide")

# AAStringSet
aa <- AAStringSet(c(
  human = "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH",
  mouse = "MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSH",
  goat  = "MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHS"
))
msaview(msa = aa, color_scheme = "clustal")

# DNAMultipleAlignment
aln <- DNAMultipleAlignment(c(
  "ATGCGATCGATCGATCG--ATCG",
  "ATGCGATCGATCGATCGATCGATCG",
  "ATGCG--CGATCGATCGATCGATCG"
), rowmask = as(IRanges(), "NormalIRanges"))
msaview(msa = aln)

After running the msa package

library(msa)
library(Biostrings)

unaligned <- readAAStringSet("proteins.fasta")
aligned <- msa(unaligned, method = "ClustalOmega")
msaview(msa = as(aligned, "AAStringSet"))

With ggtree

Pass a ggtree plot object directly as the tree argument. The phylogenetic topology is extracted automatically.

library(ggtree)
library(ape)

tree <- rtree(20)
p <- ggtree(tree) + geom_tiplab()

seqs <- setNames(
  replicate(20, paste0(sample(c("A","C","G","T"), 200, TRUE), collapse = "")),
  tree$tip.label
)

# pass the ggtree plot object directly
msaview(msa = seqs, tree = p, color_scheme = "nucleotide")

ggtree with annotations

Annotated ggtree plots work too. Only the tree topology is extracted; ggtree-specific annotations (colors, labels, metadata) stay in ggtree.

metadata <- data.frame(
  label = tree$tip.label,
  group = sample(c("A", "B", "C"), 20, replace = TRUE)
)
p2 <- ggtree(tree) %<+% metadata +
  geom_tiplab(aes(color = group)) +
  theme(legend.position = "right")

msaview(msa = seqs, tree = p2)

With treeio

library(treeio)

# treedata objects from read.beast, read.raxml, etc.
beast_tree <- read.beast("beast_output.tree")
msaview(tree = beast_tree)

# or convert from phylo
td <- as.treedata(tree)
msaview(msa = seqs, tree = td)

In Shiny

library(shiny)
library(msaviewr)

ui <- fluidPage(
  titlePanel("MSA Viewer"),
  sidebarLayout(
    sidebarPanel(
      fileInput("msa_file", "Upload alignment",
                accept = c(".fa", ".fasta", ".stock", ".sto", ".aln")),
      fileInput("tree_file", "Upload tree (optional)",
                accept = c(".nwk", ".nh", ".newick")),
      selectInput("color_scheme", "Color scheme",
                  choices = c("maeditor", "clustal", "lesk", "cinema",
                              "flower", "nucleotide", "purine_pyrimidine",
                              "clustalx_protein_dynamic",
                              "percent_identity_dynamic"),
                  selected = "maeditor"),
      actionButton("example_btn", "Load example data")
    ),
    mainPanel(
      msaviewOutput("msa_viewer", height = "600px")
    )
  )
)

server <- function(input, output, session) {
  msa_data <- reactiveVal(NULL)
  tree_data <- reactiveVal(NULL)

  observeEvent(input$msa_file, {
    msa_data(input$msa_file$datapath)
  })

  observeEvent(input$tree_file, {
    tree_data(input$tree_file$datapath)
  })

  observeEvent(input$example_btn, {
    msa_data(paste0(
      ">human\nMVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH\n",
      ">mouse\nMVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSH\n",
      ">goat\nMSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHS"
    ))
    tree_data("((human:0.1,mouse:0.2):0.05,goat:0.3);")
  })

  output$msa_viewer <- renderMsaview({
    req(msa_data())
    msaview(
      msa = msa_data(),
      tree = tree_data(),
      color_scheme = input$color_scheme
    )
  })
}

shinyApp(ui, server)

Supported inputs

Parameter Accepted types
msa File path, FASTA/Stockholm/Clustal string, named character vector, DNAStringSet, AAStringSet, RNAStringSet, DNAMultipleAlignment, AAMultipleAlignment
tree File path, Newick string, ape::phylo, treeio::treedata, ggtree plot object

Color schemes

Protein: maeditor, clustal, lesk, cinema, flower, buried, taylor, hydrophobicity, helix, strand, turn

Nucleotide: nucleotide, purine_pyrimidine, rainbow_dna, rainbow_rna

Dynamic (computed per-column): clustalx_protein_dynamic, percent_identity_dynamic

License

MIT