SOFTWARE

I have written a few programs for performing different types of analyses on codominant marker data sets. Although these are still maintained, I am moving away from developing programs in C, and moving towards creating packages and/or functions in R that take advantage of other R tools, and are more easily transportable across different operating systems.

related

PAIRWISE  RELATEDNESS  

related is an R package that allows users to estimate pairwise relatedness for individuals based on codominant molecular markers (microsatellites, SNPs, etc.), and also has simulation capabilities for comparing the performance of different estimators and for testing the resolution of a data set. Relatedness can be estimated using any of seven different methods, and can incorporate inbreeding and genotyping errors.

A tutorial for using related (including installation) can be found here.

The R manual for related can be found here.

The package can be downloaded from the link here. Instructions for which file(s) to download and how to install them can be found in the tutorial.

STORM

RELATEDNESS AND MATING PATERNS

STORM is a program written in C that uses Monte Carla simulations to test a variety of hypotheses regarding relatedness and mating patterns. Further details can be found in the manual or in the accompanying paper (Frasier (2008) Mol. Ecol. Resources 8: 1263-1266). It can be used on Windows, Mac, or Linux operating systems.

The STORM manual can be downloaded here. 

A README file with installation instructions can be downloaded here.

The program can be downloaded using the links below. In all cases, click on the “Raw” button in the link to download the file:

Windows version
Linux version

Additional instructions for installation on a Mac are here.

Some of the calculations (e.g. IR) require the genotypes to be formatted in a particular way. I have created a clunky Excel workbook that will do these conversions for you. You paste your genotype file (where the first column is individual identifiers, and the first allele for the first locus begins on column 2) into the worksheet named “PASTE”, and then get your converted genotypes from the worksheet named “RETRIEVE”. Please double-check your conversions! This Excel file can be downloaded here.

Rel-A-Tree

RELATEDNESS CLUSTERING

Rel-A-Tree is a program written in C that provides a means to cluster individuals based on relatedness values, and therefore assess patterns of relatedness without a priori information. Further details can be found in the manual. This program can be used on Windows or Linux operating systems.

The Rel-A-Tree manual can be downloaded here.

The program can be downloaded using the links below. In all cases, click on the “Raw” button in the link to download the file.