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Simulation Tools

Overview

This page has links to tools which can be used to generate simulated data suitable for challenging state-of-the-art methods in computational phylogenetics. If you would like to contribute to this list, please email tandy@cs.utexas.edu.

Tools

DAWG: DAWG is software for simulating DNA sequence evolution down a tree under the GTR+Gamma+I substitution model while also incorporating indel events.
Described in [7]

indel-Seq-Gen: indel-Seq-Gen is a modified version of Seq-Gen (v1.3.2) that creates simulated DNA and protein datasets incorporating insertion and deletion events ("indels") into its model of sequence evolution.
Described in [3, 4]

INDELible: The INDELible home page describes it as a sequence evolution tool that "can simulate evolution of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. Nucleotide simulations may use the general unrestricted model or the general time reversible model and its derivatives, and amino-acid simulations can be conducted using fifteen different empirical rate matrices."
Described in [8]

Mesquite: Mesquite is a modular software platform that enables a broad range of phylogenetic analyses. There are Mesquite packages for simulation-specific analyses, including simulation of birth-death processes, of gene trees within species trees, and of character evolution down a tree.
Described in [6]

Rose: Rose is software for simulating evolution of molecular sequences down a tree; its probabilistic evolution model incorporates both substitution and indel events.
Described in [1]

r8s: r8s is a software tool that can be used for generating simulated birth-death trees. It is also useful for estimating rates of evolution of sequences down a tree using one of several parametric or nonparametric methods.
Described in [2]

Seq-Gen: Seq-Gen can be used to simulate evolution of molecular sequences down a tree. Its models of evolution allow for different substitution rates, but indel events are not modeled.
Described in [5]

References

Disclaimer

Links to external web sites are for datasets and software available through other laboratories and organizations. The respective labs and organizations are responsible for these datasets and software; please contact them if you have any problems or questions regarding their material. If you experience any problems with our datasets or software, please feel free to contact us at tandy@cs.utexas.edu.
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