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                                                                  

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.

** Note that this package has been improved substantially since the paper was accepted. Therefore, you should download the manuals from here, rather than obtain them as “supplementary files” associated with the paper, because those are now out of date. **

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

The R manual for related can be found here: related

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

download

*Some people have had some problems loading this package into R. Solutions to these problems can be found on the Readme documentation on the download page (link above).

Family-Sim                                                                  

Family-Sim is a program Family-Sim_picwritten in C that will take an allele frequency file and use those data to generate a user-defined number of individuals of known relatedness.  Specifically, the program will generate the given number of pairs of parent-offspring, full-sibs, half-sibs, and unrelated individuals.  These data can then be used to assess the expected resolution from your data in terms of differentiating between individuals of different relatedness.  The program can be used on Windows or Linux operating systems.

The manual for Family-Sim can be downloaded here: FAMILY-SIM_Manual

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, source code.

GeNetwork                                                                  

GeNetwork is a program written in C that provides a means to conduct individual-based Screen shot 2011-09-19 at 5.00.06 PMnetwork analyses on genetic data, and to conduct simulations for hypothesis testing of the observed networks.  It was written to be used in association with the igraph package in R.  It can be used on Windows, MAC, or Linux operating systems.  I am currently testing the “power” of GeNetwork via simulations, and hopefully a paper with be forthcoming shortly.

The manual for GeNetwork can be downloaded here: GeNetwork_Manual

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, Mac versionsource code.

Rel-A-Tree                                                                  

Rel-A-Tree is a program written in C that provides a means to cluster individuals based on Rel-A-Tree_picrelatedness 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: Manual

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 versionsource code.

STORM                                                                   

STORM is a program written in C that uses Monte Carlo simulations to test a variety of STORM_pichypotheses 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: STORM_v2_Manual

A README file with installation instructions can be downloaded here: README

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 versionMac versionsource code.

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.

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