sim_normal: Simulate sequences for a given evolutionary tree, using a...
In nodeSub: Simulate DNA Alignments Using Node Substitutions
sim_normal R Documentation
Simulate sequences for a given evolutionary tree, using a standard model
of sequence evolution along the branches. Code for this function was heavily
inspired by the function simSeq from the phangorn package.
Description
Simulate sequences for a given evolutionary tree, using a standard model
of sequence evolution along the branches. Code for this function was heavily
inspired by the function simSeq from the phangorn package.
Usage
sim_normal(x, l = 1000, Q = NULL, bf = NULL, rootseq = NULL, rate = 1)
Arguments
x
a phylogenetic tree tree, i.e. an object of class
phylo
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
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
Author(s)
Klaus Schliep klaus.schliep@gmail.com
nodeSub documentation built on Nov. 14, 2023, 5:10 p.m.
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| sim_normal | R Documentation |
Simulate sequences for a given evolutionary tree, using a standard model
of sequence evolution along the branches. Code for this function was heavily
inspired by the function simSeq from the phangorn package.
Description
Simulate sequences for a given evolutionary tree, using a standard model
of sequence evolution along the branches. Code for this function was heavily
inspired by the function simSeq from the phangorn package.
Usage
sim_normal(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 |
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
Author(s)
Klaus Schliep klaus.schliep@gmail.com
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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