EVDA^{9}
Extreme
Value Domain
of Attraction
This program describes a
likelihood ratio
framework for analyzing
the fitness effects of beneficial mutations, focusing on
testing the null hypothesis that the distribution is exponential. The
principle author of this computer program is Craig Beisel.
EVOX^{3,5,8}
A
mathematical model is introduced
that aims to explain
the evolutionary process associated with the population biology
of bacterial plasmids. This model is coupled with
a statistical framework based on the maximum likelihood to estimate its
parameters and to test the associated hypotheses. The principal
authors of this computer program are Zaid Abdo and José Ponciano.
DTModSel^{2,4}
A performancebased method for selecting a likelihood
model for
phylogenetic estimation. The principle authors of this software
are Zaid Abdo, Jack Sullivan and Vlad Minin. The above link will
bring you to Jack Sullivan's webpage, where the software is
maintained.
RelioType^{1}
A maximum likelihood approach for minimizing
genotyping errors for noninvasive genetic sampling of wild
populations. The program estimates genotype reliability and
strategically directs replication at loci most likely to harbor
errors. The principal author of this software is Craig Miller.
Capwire^{6}
The use of noninvasive genetic sampling to estimate
population size in elusive or rare species is increasing. The data
generated from this sampling differ from traditional mark–recapture
data in that individuals may be captured multiple times within a
session or there may only be a single sampling event. To accommodate
this type of data, we develop a method, named capwire, based on a
simple urn model containing individuals of two capture probabilities.
The principal author of
this software is Craig Miller.
TRFLPSTATS^{7}
A statistical analysis of TRFLP data that include
objective methods for
(a) determining a baseline so that “true” peaks in electropherograms
can be identified,
(b) a means to compare electropherograms and bin fragments of similar
size,
(c) clustering algorithms that can be used to identify communities that
are similar to one another, and
(d) a means to select samples that are representative of a cluster that
can be used to
construct 16S rRNA gene clone libraries. The principal
author of these algorithms is Zaid Abdo.
Estimating overdominance^{10}. A
balanced pattern in the allele frequencies of polymorphic loci is a
potential sign of selection, particularly of overdominance. This program is associated
with Buzbas, Joyce and Abdo 2009 where Bayesian
methods to estimate selection intensity under kallele models with
overdominance is presented. The model allows for arbitrary number of
loci and alleles within a locus.
SUPPORT
These
computer programs and correponding publications
were made
possible by National Institutes of Health Grant Number P20 RR 16448
from the COBRE Program of the National Center for Research Resources
and from an NIHR01 GM07604001 on the Patterns
of Adaptive Evolution.
This computer program and corresponding publication were also partially
funded by National Science Foundation Grant Numbers DEB0089756 and
DEB 0515738.
REFERENCES
 Miller,
C., Joyce, P., Waits, L. Assessing allelic dropout and genotype
reliability using maximum likelihood, Genetics, 160: 357366,
2002.
 Minin, V, Abdo, Z.,
Joyce, P., Sullivan J., Performancebased selection of likelihood
models for phylogeny estimation. Systematic Biology, 52,(5), 672684,
2003.
 DeGelder L.,
Ponciano, J., Abdo Z., Joyce P., Forney LJ.,
and Top E. Combining
mathematical models and statistical methods to understand and predict
the dynamics of antibiotic sensitive mutants in a population of
resistant bacteria during experimental evolution, Genetics 168, (3),
11311144, 2004.
 Abdo Z, Minin
V,
Joyce P., Sullivan J. Accounting for
Uncertainty in the Tree Topology has Little
Effect on the Decision Theoretic Approach to
Model Selection in Phylogeny Estimation. Mol. Bio.
Evol, 22 (3), 691703, 2005.
 Joyce
P., Abdo Z., Ponciano J., De Gelder L, Forney L. and
Top E. Modeling the impact of periodic bottlenecks unidirectional
mutation and observational error in experimental evolution,
Journal of Mathematical Biology, 50 (6) 645652, 2005.
 C.R. Miller, P. Joyce and L.P.
Waits. A
new method for estimating
the size of small populations from genetic markrecapture
data. Molecular
Ecology 14,
19912005, 2005.
 Abdo Z., Schuette U., Bent S.,
Williams
C., Forney
LJ., Joyce P. Statistical Methods for Characterizing Diversity of
Microbial Communities by Analysis of Terminal Restriction Fragment
Length Polymorphisms of 16S rRNA genes. Environmental Microbiology 8,
(5), 929938, 2006.
 J. M.
Ponciano, L. De
Gleder, E. M. Top, P. Joyce. The population biology
of bacterial plasmids: a HiddenMarkov model approach. Genetics, 176:
957–968, 2007.
 Beisel, C.J., D. R. Rokyta, H. A.
Wichman, and P.
Joyce. Testing the extreme value domain of attraction for
distributions of beneficial fitness effects.. Genetics.176: 2441–2449, 2007.
 Buzbas,
E.O., P. Joyce, A. Abdo. Estimating selection intensity under
overdominance by Bayesian methods. Statistical
Applications in Genetics and Molecular Biology , 2009.
