Molecular Clock Simulator

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What is Clockgen

Clockgen is a simulator program that generates random nucleotide sequences based on the theory of the existence of a molecular clock. The product of clockgen is a complete phylogeny from a randomly generated (or not) ancestral sequence following simple user defined rules such as size of the sequence, model of evolution and number of mutations per generation, for as many generations as you wish (and your computer resources can handle).

The simulations behave differently from host to host according to it's immunity factor and thus, can simulate transmission models such as a transmission bottleneck.

There are many possible uses for clockgen, all of them based on the creation of a database of random clock-like sequences. These sequences can be used then to test hypothesis of real world evolution using phylogenetic reconstruction or phylodynamics analysis.

The program is freely available for academic use. Contact the author for information on how to cite the use of clockgen.

Author: Mauricio Oliveira Carneiro

What you can't do with Clockgen

Yet it is not possible to simulate recombination with clockgen. But it is a feature to be implemented in the near future. Comments and requests about what should be implemented are welcome!


The source code can be downloaded here:

clockgen-1.0.tar.bz2 (2004/07/24)

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