Programs for population genetic and relatedness calculations, and education in evolution and behavioral ecology

Developed with funding from
NSF Computational Biology
The Keck Center for Computational Biology
Rice University

NOTE: Goodnight Software applications are no longer under development. I will answer technical support questions by e-mail, but no further versions will be released.

Relatedness and Kinship will not run on Intel-based Macs or under OSX 10.5 (Leopard)

If you experience downloading problems, try using the latest version of Stuffit Expander as your browser's helper application. The latest version is always available free from Aladdin's web site.
If problems persist, e-mail for help.

Programs:

Relatedness calculates average genetic relatedness among sets of individuals defined by demographic variables, either on average or by pairs. It finds standard errors and confidence intervals for signifiance testing using a jackknife resampling method.

Features in Relatedness 5.0:

*Data sets with up to 127 loci of 127 alleles each, and number of individuals limited only by computer memory.

*Up to 32 demographic variables with complete control over the order in which they are checked.

*Pairwise values of relatedness.

*95% confidence intervals as well as standard errors.

The distribution package includes the program, a manual in Microsoft Word 6.0 format, and a sample data set. (A copy of the manual in Word 5.1 format is available on request.)

 

Relatedness 5.0 has been completely rewritten from the previous version. Users are encouraged to e-mail comments, suggestions and bug reports, and to check back here frequently for upgrades.

 

Upgrade notice:

Version 5.0.8: Fixes a bug in the new routines written for 5.0.7

Version 5.0.7: Changes treatment of missing alleles in pairwise values to match that used in average values.

Version 5.0.6: Fixes a bug which caused relatedness values to be reported as 1.0 in some cases.

Version 5.0.5: Fixes an incompatibility with System 8.5.

Version 5.0.4: Adds an option providing a shortcut for a commonly-used setting.

Version 5.0.3: Fixes a bug inadvertently introduced in the 5.0.2 update.

Version 5.0.2: Fixes a bug which caused all R' values to be set to 1.0 in some cases.

Version 5.0.1: Fixes a variety of small bugs.

An addendum to the manual includes a complete list of changes in each update.

Relatedness is available for Macintosh only

Download "Relatedness 5.0.8"

The previous version of Relatedness, 4.2c, is still available for download for comparison and double-checking of results. Download it here.

Kinship is a program to perform maximum likelihood tests of pedigree relationships between pairs of individuals in a population. The program uses genotype information for single-locus, codominant genetic markers (such as DNA microsatellite loci). The user enters two hypothetical pedigree relationships, a primary hypothesis and a null hypothesis, and the program calculates likelihood ratios comparing the two hypotheses for all possible pairs in the data set. The calculation includes a simulation procedure to determine the statistical significance of results. Kinship also calculates pairwise relatedness statistics. The distribution package includes the program, a manual in Microsoft Word 5.1 format, and a sample data set.

 

Bug Notice:

Kinship 1.0 was found to have a bug which causes incorrect results for data sets with both of the following characteristics:

1. An allele frequency block is NOT included in the file.
2. There is no group ID variable (or equivalently, a group ID variable with only 1 value).

This bug was corrected in version 1.1. If you are using Kinship 1.0 you should switch to the current version.

Kinship is available for Macintosh only

Download "Kinship 1.3.1"

Teaching Programs:

Have an idea for educational software you'd like to see for population genetics, evolution, behavioral ecology or ecology? E-mail the suggestion!

"Game Theory" demonstrates the simple Hawk/Dove/Bourgeois game designed to provide an example of the use of game theory in evolutionary theory. Students can adjust payoffs and see the resulting changes in theoretical ESS, and can then check the prediction with both stochastic and analytical simulations. The distribution package includes the program, manual and a sample homework assignment used by Joan Strassmann in her Animal Behavior class, Fall 1996.

Download "Game Theory 3.0":

For Mac OSX
For Mac Classic
For Windows

"Selection" is a straightforward population-genetic simulation demonstrating the effects of selection, drift, mutation and migration on allele frequencies in a single-locus, two allele system. The fitnesses of all 3 diploid genotypes can be independently specified, along with population size, mutation rates, migration rate, and the allele frequencies in the external population from which migrants arrive. An onscreen graph shows the results of the simulation. The distribution package includes the program and manual (although this one is straightforward enough you probably won't need the manual).

Download "Selection 3.2":

For Mac OSX
For Mac Classic
For Windows

"Sex Ratios" is a simple simulation programming for demonstrating Fisherian selection on the sex ratio. The interface is patterned on that of "Selection" (above). Users can set the cost of producing male or female offspring, the survivorship of those offspring, the amount each sex will contribute to its own future offspring, and the allocation specified by each of the competing alleles. The simulation then runs to see which of these factors influence selection and the population sex ratio.

Download "Sex Ratios 2.1"

"Bugs!" is a simple genetic algorithm program that simulates bacteria-like organisms which move about in a field of "algae" that they eat by moving over them. When they eat enough of the algae, they reproduce by division; if they don't eat enough, they die. Over time, the initial aimless bugs will evolve into efficient foragers scouring their world for fresh algae.

Download Bugs 2.0

For Mac OSX
For Mac Classic
For Windows

Biomorphs Based on an algorithm described by Richard Dawkins in his book The Blind Watchmaker, "Biomorphs" is a program to demonstrate the potential and the limitations of selection acting on genes and development. The program uses a recursive procedure to "develop" a numerical genotype into an image made of branching and overlapping lines. The program shows the user a "biomorph" image together with a set of its offspring, differing from the parent by one or a few mutations, and chooses a favorite to become the parent of the next generation. Applying artificial selection, the user can evolve interesting-- and surprisingly lifelike-- "biomorphs." There is currently no manual to this program, but with a little experimentation it shouldn't be hard to figure out.

Download Biomorphs:

For Mac OSX
For Mac Classic
For Windows

Is It Chance? Does evolution by natural selection propose that complex organs and organisms arose by mere chance? This program pits chance and selection against each other in a race to match a string of random letters to a sentence typed in by the user, and reveals clearly the difference between natural selection and "mere chance."

Download "Is It Chance?"

For Mac OSX
For Mac Classic
For Windows

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