sim_normal_explicit {nodeSub}

simulate a sequence assuming substitutions are only accumulated along the branches, using the explicit simulation method (e.g. reverse substitutions are modeled explicitly)

Description

simulate a sequence assuming substitutions are only accumulated along the branches, using the explicit simulation method (e.g. reverse substitutions are modeled explicitly)

Usage

sim_normal_explicit(x, l = 1000, Q = NULL, bf = NULL, rootseq = NULL, rate = 1)

Arguments

x

a phylogenetic tree tree, i.e. an object of class phylo or and object of class pml.

l

length of the sequence to simulate.

Q

the rate matrix.

bf

base frequencies.

rootseq

a vector of length l containing the root sequence, other root sequence is randomly generated.

rate

mutation rate or scaler for the edge length, a numerical value greater than zero.

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