sim_unlinked: Simulate a sequence assuming node substitutions are not...

In nodeSub: Simulate DNA Alignments Using Node Substitutions

Simulate a sequence assuming node substitutions are not shared amongst offspring, given two substitution matrices: one for substitutions occuring on the nodes, and one for substitutions occuring along the branches.

Description

Simulate a sequence assuming node substitutions are not shared amongst offspring, given two substitution matrices: one for substitutions occuring on the nodes, and one for substitutions occuring along the branches.

Usage

sim_unlinked(
  phy,
  Q1 = rep(1, 6),
  Q2 = rep(1, 6),
  rate1 = 0.1,
  rate2 = 0.1,
  l = 1000,
  bf = rep(0.25, 4),
  rootseq = NULL,
  node_time = 0.001
)

Arguments

phy	tree for which to simulate sequences
Q1	substitution matrix along the branches, default = JC
Q2	substitution matrix on the nodes, default = JC
rate1	mutation rate along the branch, default = 0.1
rate2	mutation rate on the node, default = 0.1
l	number of base pairs to simulate
bf	base frequencies, default = c(0.25, 0.25, 0.25, 0.25)
rootseq	sequence at the root, simulated by default
node_time	amount of time spent at the nodes

Value

list with four items

1. alignment Phydat object with the resulting alignment

2. rootseq the rootsequence used

3. total_branch_substitutions total number of substitutions accumulated on the branches

4. total_node_substitutions total number of substitutions accumulated at the nodes

nodeSub documentation built on Nov. 14, 2023, 5:10 p.m.