genTrees: Generate permuted trees using rNNI or rtree, and check for...
In RADami: Phylogenetic Analysis of RADseq Data

Description Usage Arguments Details Value Author(s) See Also Examples

This function generates a specified number of trees by permutation or random generation, then checks to make sure that they are unique before returning the original tree plus the generated trees

1 2	genTrees(x, N = 200, filebase = "trial", method = c("nni", "random"), maxmoves = 2, perms = "DEFAULT", software = c("raxml"), ...)

`x`	an object of class `"phylo"`
`N`	number of new trees to return
`filebase`	base name of the file to which trees will be written
`method`	method of generating the trees, either nearest neighbor interchange (nni) or random
`maxmoves`	maximum number nni moves
`perms`	number of permutations per nni stratum; defaults to the number of single-step nni trees, then the remainder of N divided by the number of nni strata requested (negatives not allowed)
`software`	not currently used; in an earlier version, would write out analysis file for PAUP or RAxML
`...`	further arguments to be passed to rtree

The main need for this function is to ensure that the trees you get back are unique... mainly just a wrapper to rNNI and rtree. perms defaults to:

c(length(nni(x)), max(1, as.integer(N - (length(nni(x))))))

an object of class "multiPhylo"

Andrew Hipp

gen.RAD.loci.datasets, compare.all.trees

  data(oak.tree)
  out <- genTrees(oak.tree, N = 10, maxmoves = 2, perms = c(5, 5))
  plot(out[[1]]) # this is the tree you input
  plot(out[[2]]) # this is the first generated tree...
  plot(out[[11]]) # ... and this is the last generated tree.