Electronic resources to PhD thesis of Simon Aeschbacher

SPoCS

SPoCS is a software to Simulate Populations under Complex Scenarios. It is individual-based and simulates pedigrees and genetics of a set of populations forward in time. The populations are called demes in the following. SPoCS has been implemented in Java.

Demography and migration

The demography is specified by a trajectory of census deme sizes for each deme, and a list of transfer events at specific times. During a transfer event, a number of individuals as specified by the user is taken from a desired deme and moved to another deme. New demes are founded via transfer events; exisiting demes may receive further individuals via transfer events later. Transfer numbers may be specified separately for females and males.

Demes may exchange migrants according to an arbitrary matrix of emigration rates. Separate matrices must be specified for females and males.

Genetics

Genetics follow the rules of Mendelian inheritance for diploid organisms. Each individual has a phased genotype with a number of microsatellites specified by the user. Mutation may follow either the k-alleles model (KAM) of mutation or the two-phase model (TPM) of mutation, where a locus mutates with a certain probability according to the single-stepwise model of mutation and otherwhise according to the generalized stepwise model of mutation. Each locus has its own mutation rate. Initial allele frequencies may be set manually, or sampled under various assumptions. No recombination and no selection has been implemented so far.

Executable files and an example

A .zip file (1.4 MB) with a JAR file (Java ARchive) of SPoCS, an example and a readme.txt file are provided here. The JAR file SPoCS.jar contains Java bytecode files (.class files) that can be read independently of the computer platform, provided you have a Java Virtual Machine (JVM) installed.

The example contains the various input files needed. These illustrate the required format and contain data coming from a subset of the Alpine ibex demes studied in the thesis. The readme.txt file explains how to use SPoCS either in the interactive mode or in the command-line only mode.

Source code and API

The Java source code (.java files) is available here as a compressed file (src.tar.gz, 293 KB). Further, an API (application programming interface) can be accessed here.