Skip Navigation



Bioinformatics Advance Access published online on January 12, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk051
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
22/6/768    most recent
btk051v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Kuhner, M. K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kuhner, M. K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 15, 2005
Revised January 9, 2006
Accepted January 5, 2006

Applications note

LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters

Mary K. Kuhner 1 *

1 Department of Genome Sciences, Box 357730, University of Washington, Seattle, WA 98195-7730, USA

* To whom correspondence should be addressed.
Mary K. Kuhner, E-mail: lamarc{at}gs.washington.edu


  Abstract

Summary: We present a Markov chain Monte Carlo coalescent genealogy sampler, LAMARC 2.0, which estimates population genetic parameters from genetic data. LAMARC can co-estimate subpopulation {Theta} = 4Neµ, immigration rates, subpopulation exponential growth rates, and overall recombination rate, or a user-specified subset of these parameters. It can perform either maximum-likelihood or Bayesian analysis, and accomodates nucleotide sequence, SNP, microsatellite or elecrophoretic data, with resolved or unresolved haplotypes. It is available as portable source code and executables for all three major platforms.

Availability: LAMARC 2.0 is freely available at: http://evolution.gs.washington.edu/lamarc.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 ANN BOT (LOND)Home page
R. G. Collevatti, S. G. Rabelo, and R. F. Vieira
Phylogeography and disjunct distribution in Lychnophora ericoides (Asteraceae), an endangered cerrado shrub species
Ann. Bot., September 1, 2009; 104(4): 655 - 664.
[Abstract] [Full Text] [PDF]

Home page
 J MOLLUS STUDHome page
S. Giokas, D. Thomaz, V. Douris, R. lecanidou, and G. C. Rodakis
5000 YEARS OF MOLECULAR EVOLUTION IN A POPULATION OF THE LAND SNAIL ALBINARIA CAERULEA TRANSPORTED BY HUMANS
J. Mollus. Stud., August 18, 2009; (2009) eyp041v1.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. J. White and N. J. Gemmell
Can Indirect Tests Detect a Known Recombination Event in Human mtDNA?
Mol. Biol. Evol., July 1, 2009; 26(7): 1435 - 1439.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
P. E. Marek and J. E. Bond
A Mullerian mimicry ring in Appalachian millipedes
PNAS, June 16, 2009; 106(24): 9755 - 9760.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. R. Omilian and M. Lynch
Patterns of Intraspecific DNA Variation in the Daphnia Nuclear Genome
Genetics, May 1, 2009; 182(1): 325 - 336.
[Abstract] [Full Text] [PDF]

Home page
 ANN BOT (LOND)Home page
S. G. Byars, Y. Parsons, and A. A. Hoffmann
Effect of altitude on the genetic structure of an Alpine grass, Poa hiemata
Ann. Bot., April 1, 2009; 103(6): 885 - 899.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. Ross-Ibarra, M. Tenaillon, and B. S. Gaut
Historical Divergence and Gene Flow in the Genus Zea
Genetics, April 1, 2009; 181(4): 1399 - 1413.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
K. G. McCracken, M. Bulgarella, K. P. Johnson, M. K. Kuhner, J. Trucco, T. H. Valqui, R. E. Wilson, and J. L. Peters
Gene Flow in the Face of Countervailing Selection: Adaptation to High-Altitude Hypoxia in the {beta}A Hemoglobin Subunit of Yellow-Billed Pintails in the Andes
Mol. Biol. Evol., April 1, 2009; 26(4): 815 - 827.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
D. E. Janes, T. Ezaz, J. A. Marshall Graves, and S. V. Edwards
Recombination and Nucleotide Diversity in the Sex Chromosomal Pseudoautosomal Region of the Emu, Dromaius novaehollandiae
J. Hered., March 1, 2009; 100(2): 125 - 136.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C. N. Balakrishnan and S. V. Edwards
Nucleotide Variation, Linkage Disequilibrium and Founder-Facilitated Speciation in Wild Populations of the Zebra Finch (Taeniopygia guttata)
Genetics, February 1, 2009; 181(2): 645 - 660.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
W. Delport, K. Scheffler, and C. Seoighe
Models of coding sequence evolution
Brief Bioinform, January 1, 2009; 10(1): 97 - 109.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
G. Tezanos-Pinto, C. S. Baker, K. Russell, K. Martien, R. W. Baird, A. Hutt, G. Stone, A. A. Mignucci-Giannoni, S. Caballero, T. Endo, et al.
A Worldwide Perspective on the Population Structure and Genetic Diversity of Bottlenose Dolphins (Tursiops truncatus) in New Zealand
J. Hered., January 1, 2009; 100(1): 11 - 24.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. Naderi, H.-R. Rezaei, F. Pompanon, M. G. B. Blum, R. Negrini, H.-R. Naghash, O. Balkiz, M. Mashkour, O. E. Gaggiotti, P. Ajmone-Marsan, et al.
The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals
PNAS, November 18, 2008; 105(46): 17659 - 17664.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. R. Omilian, D. G. Scofield, and M. Lynch
Intron Presence-Absence Polymorphisms in Daphnia
Mol. Biol. Evol., October 1, 2008; 25(10): 2129 - 2139.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
A. R. Lemmon and E. M. Lemmon
A Likelihood Framework for Estimating Phylogeographic History on a Continuous Landscape
Syst Biol, August 1, 2008; 57(4): 544 - 561.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
B. F. Keele, L. Tazi, S. Gartner, Y. Liu, T. B. Burgon, J. D. Estes, T. C. Thacker, K. A. Crandall, J. C. McArthur, and G. F. Burton
Characterization of the Follicular Dendritic Cell Reservoir of Human Immunodeficiency Virus Type 1
J. Virol., June 1, 2008; 82(11): 5548 - 5561.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
C. E. Valdiosera, J. L. Garcia-Garitagoitia, N. Garcia, I. Doadrio, M. G. Thomas, C. Hanni, J.-L. Arsuaga, I. Barnes, M. Hofreiter, L. Orlando, et al.
From the Cover: Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos)
PNAS, April 1, 2008; 105(13): 5123 - 5128.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. E. Alter, E. Rynes, and S. R. Palumbi
DNA evidence for historic population size and past ecosystem impacts of gray whales
PNAS, September 18, 2007; 104(38): 15162 - 15167.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
D. A. Moeller, M. I. Tenaillon, and P. Tiffin
Population Structure and Its Effects on Patterns of Nucleotide Polymorphism in Teosinte (Zea mays ssp. parviglumis)
Genetics, July 1, 2007; 176(3): 1799 - 1809.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. K. Kuhner
Robustness of Coalescent Estimators to Between-Lineage Mutation Rate Variation
Mol. Biol. Evol., December 1, 2006; 23(12): 2355 - 2360.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.