Simulations made simple
Marlin is a Mac-only program for running spatially explicit forward-in-time population genetic simulations of both neutral genetic markers and quantitative traits under selection. It provides an intuitive user interface with realistic geographic scenarios can easily be easily created and simulated. But Marlin goes further than that and directly analyses and plots the results. This combination of creation, simulation, and analysis makes Marlin ideal for teaching and for scientists who are interested in doing simulations without having to learn command-line operations.
To learn more about Marlin, click here to view the Help-files.
 Set-up the metapopulation as a map
Marlin allows you to easily create geographically realistic metapopulation lay-outs. Defining populations is as easy as clicking their location on a grid. For more complex geographical scenarios, the metapopulation lay-out can be loaded from an image file, for example a species' distribution map. Besides the direct drawing of the metapopulation, Marlin gives easy access to many different simulation parameters, allowing you to specify in great detail the characteristics of the simulated organisms, populations, and genetic markers.
 Intuitive user interface
The polished interface makes it easy to set change the simulation parameters even for novice users. The bar on the left-hand side of the window separates the many parameters into logical groups and gives direct access to the results. Marlin also has a tabbed interface that lets you quickly switch between runs,
 Directly analyse and view your results
Marlin can plot the values of many different summary statistics directly when the run is finished. This allows you for example to track the value of Fst or Qst as a function of the number of generations. Other combinations are also possible, such as plotting the relationship between Fis and the population size, or between the heterozygosity and the population size. For spatially explicit scenarios, Marlin can graph the results, for example producing a spatial map of the trait value of a quantitative trait under spatially varying selection. Maps can be created for different generations, allowing you to see the development of the population structure over time.
 Store scenarios as presets
Marlin allows the user to store the simulation settings as presets that can be easily used for starting new runs. This provides a fast way to have multiple runs with the same settings. Settings can also be exported and imported so they can be shared among users. This can for example be used for distributing a simulation scenario among all students’ computers in a practical. Marlin has several default presets that represent interesting demographic scenarios.
 Solid foundation
Technically, Marlin provides a front end for the simulation software QuantiNemo, developed by Samuel Neuenschwander. This provides a solid and thoroughly tested foundation for the simulations. However, Marlin does not encompass all of QuantiNemo’s many abilities; for example, QuantiNemo allows the use of an explicit genetic map, but Marlin does not. Settings-files can be exported for use by QuantiNemo, for example for running simulations on a computer cluster. In this way, the user-friendly interface of Marlin can be combined with the power of the commandline.
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