无法保存plotBS()输出的树数据——基于phyDat序列构建进化树的问题

Got it, I've run into this exact issue before with phangorn's plotBS()! The key thing most people miss is that plotBS() actually returns a modified phylogenetic tree object (with bootstrap values attached as node labels) — you just need to capture that return value instead of only running the function to plot. Here's how to do it step-by-step with your data:

Step 1: Complete Tree Construction & Bootstrap Analysis (if you haven't already) #

First, let's tie together your existing sequence data with tree building and bootstrap testing (adjust the tree-building method if you used something like maximum likelihood instead of NJ):

library(seqinr)
library(phangorn)
library(ape) # Needed for tree-saving functions

# Your original sequence setup
seqs <- DNAMultipleAlignment( 
  c(a1 = "------ATGTTCATTAACCGCTGACTATTCTCAACCA", 
    a2 = "------ATGTTCACCGACCGCTGACTATTCTCTACAA", 
    a3 = "---GTGACCTTCATCAACCGATGATTATTCTCAA---", 
    a4 = "---TCAGTCGTCACCAGGCGTTG-CAGGACCCGAC--", 
    a5 = "ATGGGGGTCTTCCTCA-TCGCCGTCGCCGCGT-----"))
phyDat_seqs <- as.phyDat(seqs)

# Build initial tree (example: Neighbor-Joining)
dm <- dist.ml(phyDat_seqs)
base_tree <- NJ(dm)

# Run bootstrap replicates (adjust `bs` to your desired number of replicates)
bs_replicates <- bootstrap.phyDat(phyDat_seqs, 
                                  FUN = function(x) NJ(dist.ml(x)), 
                                  bs = 100)

Step 2: Capture the Bootstrap Tree from plotBS() #

Instead of just running plotBS() to visualize, assign its output to a variable — this variable will hold your tree with bootstrap values embedded:

# Plot the bootstrap tree AND capture the tree object
bootstrap_tree <- plotBS(base_tree, bs_replicates, 
                         type = "phylogram", # Adjust plot type as needed
                         bs.col = "blue",    # Customize bootstrap text color
                         bs.adj = 0.5)       # Adjust bootstrap text position

Step 3: Save the Bootstrap Tree to File #

Now use ape package functions to write the tree to a standard phylogenetic file format (Newick or Nexus):

# Save as Newick format (most common for tree viewers)
write.tree(bootstrap_tree, file = "bootstrap_tree.nwk")

# OR save as Nexus format
write.nexus(bootstrap_tree, file = "bootstrap_tree.nex")

Key Notes: #

• The bootstrap_tree object is a standard phylo class object, so any tree-manipulation or saving function that works with phylo objects will work here.
• Bootstrap values are stored in the node.label slot of the bootstrap_tree object — you can verify this with bootstrap_tree$node.label.

内容的提问来源于stack exchange，提问作者Mel