Bioinformatics Vol. 18 no. 10 2002
Pages 1404-1405
© 2002 Oxford University Press
Applications Note |
GENIE: estimating demographic history from molecular phylogenies
1 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Received on February 15, 2002
; revised on April 12, 2002
; accepted on April 17, 2002
Summary: GENIE implements a statistical framework for inferring the demographic history of a population from phylogenies that have been reconstructed from sampled DNA sequences. The methods are based on population genetic models known collectively as coalescent theory.
Availability: GENIE is available from http://evolve.zoo.ox.ac.uk. All popular operating systems are supported.
Contact: oliver.pybus{at}zoo.ox.ac.uk
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. G. Moyle, C. E. Filardi, C. E. Smith, and J. Diamond Explosive Pleistocene diversification and hemispheric expansion of a "great speciator" PNAS, February 10, 2009; 106(6): 1863 - 1868. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Provan, G. E Beatty, S. L Keating, C. A Maggs, and G. Savidge High dispersal potential has maintained long-term population stability in the North Atlantic copepod Calanus finmarchicus Proc R Soc B, January 22, 2009; 276(1655): 301 - 307. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Soria-Carrasco and J. Castresana Estimation of Phylogenetic Inconsistencies in the Three Domains of Life Mol. Biol. Evol., November 1, 2008; 25(11): 2319 - 2329. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. N. Minin, E. W. Bloomquist, and M. A. Suchard Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics Mol. Biol. Evol., July 1, 2008; 25(7): 1459 - 1471. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. M. Hines Historical Biogeography, Divergence Times, and Diversification Patterns of Bumble Bees (Hymenoptera: Apidae: Bombus) Syst Biol, February 1, 2008; 57(1): 58 - 75. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Wirth, G. Morelli, B. Kusecek, A. van Belkum, C. van der Schee, A. Meyer, and M. Achtman The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis Genome Res., November 1, 2007; 17(11): 1647 - 1656. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Tanaka, K. Hanada, H. Hanabusa, F. Kurbanov, T. Gojobori, and M. Mizokami Increasing genetic diversity of hepatitis C virus in haemophiliacs with human immunodeficiency virus coinfection J. Gen. Virol., September 1, 2007; 88(9): 2513 - 2519. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Jimenez-Hernandez, M. Torres-Puente, M. A. Bracho, I. Garcia-Robles, E. Ortega, J. del Olmo, F. Carnicer, F. Gonzalez-Candelas, and A. Moya Epidemic dynamics of two coexisting hepatitis C virus subtypes J. Gen. Virol., January 1, 2007; 88(1): 123 - 133. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C.-C. Hon, T.-Y. Lam, A. Drummond, A. Rambaut, Y.-F. Lee, C.-W. Yip, F. Zeng, P.-Y. Lam, P. T. W. Ng, and F. C. C. Leung Phylogenetic Analysis Reveals a Correlation between the Expansion of Very Virulent Infectious Bursal Disease Virus and Reassortment of Its Genome Segment B. J. Virol., September 1, 2006; 80(17): 8503 - 8509. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. J. Etherington, S. M. Ring, M. A. Charleston, J. Dicks, V. J. Rayward-Smith, and I. N. Roberts Tracing the origin and co-phylogeny of the caliciviruses. J. Gen. Virol., May 1, 2006; 87(Pt 5): 1229 - 1235. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Tanaka, K. Takahashi, E. Orito, Y. Karino, J.-H. Kang, K. Suzuki, A. Matsui, A. Hori, H. Matsuda, H. Sakugawa, et al. Molecular tracing of Japan-indigenous hepatitis E viruses. J. Gen. Virol., April 1, 2006; 87(Pt 4): 949 - 954. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Goodreau Assessing the Effects of Human Mixing Patterns on Human Immunodeficiency Virus-1 Interhost Phylogenetics Through Social Network Simulation. Genetics, April 1, 2006; 172(4): 2033 - 2045. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. T. Herbeck, D. C. Nickle, G. H. Learn, G. S. Gottlieb, M. E. Curlin, L. Heath, and J. I. Mullins Human Immunodeficiency Virus Type 1 env Evolves toward Ancestral States upon Transmission to a New Host J. Virol., February 15, 2006; 80(4): 1637 - 1644. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Nakano, L. Lu, Y. He, Y. Fu, B. H. Robertson, and O. G. Pybus Population genetic history of hepatitis C virus 1b infection in China J. Gen. Virol., January 1, 2006; 87(1): 73 - 82. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Salemi, S. L. Lamers, S. Yu, T. de Oliveira, W. M. Fitch, and M. S. McGrath Phylodynamic Analysis of Human Immunodeficiency Virus Type 1 in Distinct Brain Compartments Provides a Model for the Neuropathogenesis of AIDS J. Virol., September 1, 2005; 79(17): 11343 - 11352. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Drummond, A. Rambaut, B. Shapiro, and O. G. Pybus Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences Mol. Biol. Evol., May 1, 2005; 22(5): 1185 - 1192. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Hue, D. Pillay, J. P. Clewley, and O. G. Pybus Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups PNAS, March 22, 2005; 102(12): 4425 - 4429. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Lemey, O. G. Pybus, A. Rambaut, A. J. Drummond, D. L. Robertson, P. Roques, M. Worobey, and A.-M. Vandamme The Molecular Population Genetics of HIV-1 Group O Genetics, July 1, 2004; 167(3): 1059 - 1068. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. S. Flanagan, A. Tobler, A. Davison, O. G. Pybus, D. D. Kapan, S. Planas, M. Linares, D. Heckel, and W. O. McMillan Historical demography of Mullerian mimicry in the neotropical Heliconius butterflies PNAS, June 29, 2004; 101(26): 9704 - 9709. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. F. Sarkar and D. S. Guttman Evolution of the Core Genome of Pseudomonas syringae, a Highly Clonal, Endemic Plant Pathogen Appl. Envir. Microbiol., April 1, 2004; 70(4): 1999 - 2012. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. E. Robbins, P. Lemey, O. G. Pybus, H. W. Jaffe, A. S. Youngpairoj, T. M. Brown, M. Salemi, A.-M. Vandamme, and M. L. Kalish U.S. Human Immunodeficiency Virus Type 1 Epidemic: Date of Origin, Population History, and Characterization of Early Strains J. Virol., June 1, 2003; 77(11): 6359 - 6366. [Abstract] [Full Text] [PDF]
|
|