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Paul Joyce

University of Idaho


Computer Programs



EVDA9  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.


EVO-X3,5,8   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.

DT-ModSel2,4 A performance-based 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.

RelioType1  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.

Capwire6  The use of non-invasive 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.

TRFLP-STATS7  A statistical analysis of T-RFLP 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 overdominance10.  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 k-allele 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 NIH-R01 GM076040-01 on the Patterns of Adaptive Evolution.

This computer program and corresponding publication were also partially funded by National Science Foundation Grant Numbers DEB-0089756 and DEB- 0515738.


 
REFERENCES

  1. Miller, C., Joyce, P.,  Waits, L. Assessing allelic dropout and genotype reliability using maximum  likelihood, Genetics, 160: 357-366, 2002.
  2. Minin, V, Abdo, Z., Joyce, P., Sullivan J., Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology, 52,(5), 672-684, 2003.
  3. 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), 1131-1144, 2004.
  4. 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), 691-703, 2005.
  5. 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) 645-652, 2005.        
  6. C.R. Miller, P. Joyce and L.P. Waits.  A new method for estimating the size of small populations from genetic mark-recapture data.   Molecular Ecology 14, 1991-2005, 2005.
  7. 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), 929-938, 2006.
  8. J. M. Ponciano,  L. De Gleder, E. M. Top, P. Joyce.  The population biology of bacterial plasmids:  a Hidden-Markov model approach.  Genetics, 176: 957–968,  2007.
  9. 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.
  10. Buzbas, E.O., P. Joyce, A. Abdo.  Estimating selection intensity under overdominance by Bayesian methods.  Statistical Applications in Genetics and Molecular Biology , 2009.