sim_linked: simulate a sequence assuming conditional substitutions on the...

In thijsjanzen/nodeSub: Simulate DNA Alignments Using Node Substitutions

simulate a sequence assuming conditional substitutions on the node.

Description

simulate a sequence assuming conditional substitutions on the node.

Usage

sim_linked(
  phy,
  Q = rep(1, 6),
  rate = 0.1,
  node_mut_rate_double = 1e-09,
  l = 1000,
  bf = rep(0.25, 4),
  rootseq = NULL,
  node_time = 0.01
)

Arguments

phy	tree for which to simulate sequences
Q	substitution matrix along the branches, default = JC
rate	mutation rate , default = 1
node_mut_rate_double	mutation rate on the node, default = 1e-9
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	time spent at the node

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

thijsjanzen/nodeSub documentation built on Nov. 15, 2023, 2:44 p.m.