How To Make A Phylogenetic Tree From A Binary Matrix

Question

[Diego D.]

Hello :)

I need to generate a phylogenetic tree from a binary matrix.

First, i mapped the reads to the reference genome, then, i made the SNP calling with samtools, finally, i wrote a small script in perl to construct the matrix.

I have seen that there is a R package called "ape" that i can use for this purpose. I downloaded and installed it, but i don't know how to use it, i don't know much about R.

Anyone know how to get the tree from the binary matrix with ape?

thanks in advance.

[beroe1]

Related question here

Answer 1

[gdevailly]

I know that this is a really old question, but still it comes pretty early in my google search, I though I'd give you my solution:

library(ape)
mat <- matrix(
    c(
      1,1,1,1,1,1,1,
      0,0,1,0,1,0,1,
      0,0,1,0,0,0,1,
      1,1,1,0,1,1,1,
      0,0,0,0,0,0,0

    ), byrow = TRUE, nrow = 5, dimnames = list(paste0("r", 1:5), paste0("c", 1:7))
)

mat.nj <- nj(dist.gene(mat)) # neighbour joining tree construction
plot(mat.nj, "phylo") # we plot it
nodelabels() # we id node label

# internal node state reconstruction
MPR(mat[,1], mat.nj, outgroup = "r1") # this give us the value of all internal nodes for c1 assuming root of the tree is r1

# lapply magic to call MPR on all character/gene/whatever
internalNodes <- lapply(seq_len(ncol(mat)), function(x) MPR(mat[, x], mat.nj, outgroup = "r1")[, 1, drop = FALSE])
internalNodes <- do.call(cbind, internalNodes)

Answer 2

[Adrian Pelin]

The Phylip package has something. but if you find how to do it with ape, I am interested to know.