Seq-Gen is a widely used bioinformatic program designed for the Monte Carlo simulation of molecular sequence evolution along a provided phylogenetic tree. Developed by Andrew Rambaut and Neil C. Grassly, it allows researchers to simulate how DNA, RNA, or amino acid sequences mutate over time given a specific phylogenetic history.
The official software page hosted by the University of Edinburgh can be accessed via the Seq-Gen Official Homepage. Core Functionality
Input Mechanisms: It reads user-supplied phylogenetic trees in the standard Newick format.
Evolutionary Models: Supports common models of sequence substitution, including the General Reversible (GTR) model, HKY, and various amino acid substitution models.
Rate Heterogeneity: Incorporates site-specific rate variations (such as gamma distributions) to model realistic sequence evolution.
High-Throughput Output: Capable of reading any number of trees and producing multiple independent replicate data sets for each tree, which is ideal for statistical benchmarking.
Reproducibility: By specifying a dedicated random seed number, users can perfectly regenerate identical simulated sequence datasets. Usage and Availability