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
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
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
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.
Version 5.0.8: Fixes a bug in the new routines written for
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
Version 5.0.3: Fixes a bug inadvertently introduced in the
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.
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.
Kinship 1.0 was found to have a bug which
causes incorrect results for data sets with both of the following
An allele frequency block is NOT included in the file.
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.
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.
"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).
"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.
"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.
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.
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