activate_seqgen

The path of the seqgen binary that will be used
for simulations.

binary

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

priority

This allows you to use seq-gen to simulate finite sites mutation models.
You need to download the program from
<url>http://tree.bio.ed.ac.uk/software/seqgen/</url>
and compile the binary first.

Coalescent simulators can rapidly simulate biological sequences
    evolving according to a given model of evolution.
    This package allows to specify such models, transparently calls a suitable
    simulator, parses the results and calculates additional summary statistics.
    It supports the simulators 'ms', 'msms' and 'scrm' and can simulate
    finite-sites mutation models by combining the simulators with the program
    'seq-gen'.

Paul Staab

coala

A Framework for Coalescent Simulation

activate_seqgen function

Andrew Rambaut and Nicholas C. Grass.
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

activate_seqgen: Use seq-gen for simulating finite sites mutation models

Description

Usage

Arguments

Citation