sim_normal_explicit: simulate a sequence assuming substitutions are only...

In thijsjanzen/nodeSub: Simulate DNA Alignments Using Node Substitutions

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

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