simulator_seqgen {coala}

Simulator: seq-gen

Description

This allows you to use seq-gen to simulate finite sites mutation models. When using seq-gen, coala will simulate ancestral tress using the other simulators, and call seq-gen to simulate finite sites mutations using the trees. Seq-gen has a low priority, but will always be used when finite sites mutation models are used.

Usage

activate_seqgen(binary = NULL, priority = 100)

Arguments

binary

The path of the seqgen binary that will be used for simulations. If none is provided, coala will look for a binary called 'seqgen' or 'seq-gen' using the PATH variable.

priority

The priority for this simulator. If multiple simulators can simulate a model, the one with the highest priority will be used.

Installation

You need to download the program from http://tree.bio.ed.ac.uk/software/seqgen/ and compile the binary prior to invoking this function. On Debian-based systems, you can alternatively install the package 'seg-gen'.

References

Andrew Rambaut and Nicholas C. Grassly. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci (1997) 13 (3): 235-238 doi:10.1093/bioinformatics/13.3.235

See Also

Other simulators: simulator_ms, simulator_msms, simulator_scrm

Examples

## Not run: activate_seqgen("./bin/seqgen")