simulate_dna: Simulate DNA sequence alignment

In thednainus/sarscov2simulations: Script to simulate phylogenetic trees and sequence data for SARS-CoV-2

Simulate DNA sequence alignment

Description

Function to simulate DNA sequence alignment based on the HKY DNA substitution model

Usage

simulate_dna(tree)

Arguments

tree	object of class phylo

Details

This function will simulate DNA sequence alignment using seq-gen http://tree.bio.ed.ac.uk/software/seqgen/. Parameters used in this function are: -mHKY: selects the model. Here we select HKY DNA substitution model -l29500: selects the length of the DNA sequence alignment to simulate. Here alignments will have 29500 base pairs. -t5.5: selects the transition/tranversion rate -f0.3,0.2,0.2,0.3 selects the frequency of each nucleotide in the sequence alignment in the order of A, C, G, T. Parameters -t and -f must be set when simulating HKY substitution models -s0.001 scale branch lengths in order to make then equal to the expected number of substitution per site for each branch. -or: Return alignment as a relaxed PHYLIP format. With this option sequence names can have more than 10 characters.

Value

DNA sequence alignment in PHYLIP format

Examples

TO DO

thednainus/sarscov2simulations documentation built on Feb. 9, 2023, 2:12 p.m.