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A forward-time simulator for gene sequences modeling a variety of mutation and selection processes.
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README.md

santa-sim

SANTA is JAVA software application that simulates the evolution of a population of gene sequences forwards through time. It models the underlying biological processes as discrete components; replication (including recombination), mutation (including indels), fitness and selection. SANTA is easy to use and is well-suited to simulate pathogen evolution according to different scenarios.

A pre-built cross-platform executable jar file (santa.jar) for SANTA-SIM v1.0 is available at the Releases page.

To download and build the project from source code, please execute the following command:

git clone https://github.com/santa-dev/santa-sim
ant

Detailed information on how to use SANTA is available at the wiki page. Several example simulation configuration files (.xml) are inside the examples directory.

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