blastar (version 0.1.1)

build_nj_tree: Build a Neighbor-Joining tree from a multiple sequence alignment

Description

This function takes a Multiple Sequence Alignment (MSA) object (e.g., output of align_sequences(method = "msa")) and generates a Neighbor-Joining (NJ) tree.

Usage

build_nj_tree(msa, model = "raw", pairwise.deletion = TRUE)

Value

An object of class phylo (NJ tree)

Arguments

msa

A multiple alignment object (class MsaDNAMultipleAlignment or similar)

model

Evolutionary model for distance calculation passed to ape::dist.dna (e.g., "raw", "JC69", "K80", etc.)

pairwise.deletion

Logical. If TRUE, compute distances with pairwise deletion

Examples

# \donttest{
# Build NJ tree from multiple sequence alignment (requires msa package)
if (requireNamespace("msa", quietly = TRUE)) {
  # Create example sequences
  df <- data.frame(
    accession = c("seq1", "seq2", "seq3"),
    sequence = c("ATGCATGC", "ATGCTAGC", "ATGGATGC")
  )
  
  # Generate MSA
  msa_result <- align_sequences(df, method = "msa", msa_method = "ClustalOmega")
  
  # Build NJ tree
  tree <- build_nj_tree(msa_result, model = "raw")
  print(tree)
}
# }