SPIP Software

Description

SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user. Numerous variables controlling the age structure of the population, the number of offspring produced, the variance in male and female reproductive success, survival rates of different age classes, mate fidelity, duration of simulation, etc. can be specified by the user. The program stores the pedigree of all individuals in the simulated population. This pedigree is used to simulate genetic data on sampled individuals by tracing lineages back through paternal or maternal genes within each sampled individual. Data may be simulated for an arbitrary number of loci that are assumed to be independently segregating and to not be subject to natural selection, nor linked to any selected genes. Genotypes are reported in terms of both "founder alleles" (i.e., each distinct allele amongst the founders of the pedigree is given a distinct label) and also in terms of alleles whose frequencies amongst the founding members of the pedigree may be specified by the user. The pedigree of individuals is also output by spip in a format that may be read into programs of the MORGAN package maintained by Elizabeth A. Thompson at the Department of Statistics, University of Washington. Particularly useful, in this regard, the pedigree output from spip may be fed into the MORGAN program kin and the coefficients of inbreeding for sampled individuals may be computed exactly, given the pedigree, as well as coefficients of coancestry for pairs of individuals. (Doing so requires first counting the pedigree components, which is possible using a version of the kin program that I (Eric C. Anderson) have modified, called count_ped_cmps.)

Software

All versions include the source code, documentation, and example files. The Mac OS X and Windows versions also include binaries for those operating systems.

Source code: spip.tar.gz (316 Kb)

Mac OS X: spipOSX.tar.gz (384 Kb)

Windows: spipPC.zip (391 Kb)

Documentation

This software accompanies the following journal article:

Anderson, E. C., and K. K. Dunham.
2005. SPIP 1.0: a program for simulating pedigrees and genetic data in age-structured populations. Molecular Ecology Notes 5(2):459-461.
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Registration

Software registration is optional. However, we like to know who is using it and for what purpose so that we may develop our software in a manner that is useful to you. Your information will not be distributed to anyone else.

To register, send an email to Eric Anderson with the following information:

  • name
  • email address
  • affiliation
  • how you plan to use the program
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Last modified: 12/24/2014