sim_normal_explicit {nodeSub} | R Documentation |
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 |
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
alignment Phydat object with the resulting alignment
rootseq the rootsequence used
total_branch_substitutions total number of substitutions accumulated on the branches
total_node_substitutions total number of substitutions accumulated at the nodes