Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
Department of Zoology, University of Oxford South Parks Road, Oxford OX1 3PS, UK
1 To whom correspondence should be addressed.
Motivation: Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity can also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus, large sets of replicate simulations can be easily created. This can be used to test phylogenetic hypotheses using the parametric bootstrap.
Availability: Seq-Gen can be obtained by WWW from http://evolve.zoo.ox.ac.uk/Seq-Gen/seq-gen.html or by FTP from ftp://evolve.zoo.ox.ac.uk/packages/Seq-Gen/. The package includes the source code, manual and example files. An Apple Macintosh version is available from the same sites.
Received on August 22, 1996; revised on October 30, 1996; accepted on October 30, 1996
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N. A. Doria-Rose, G. H. Learn, A. G. Rodrigo, D. C. Nickle, F. Li, M. Mahalanabis, M. T. Hensel, S. McLaughlin, P. F. Edmonson, D. Montefiori, et al. Human Immunodeficiency Virus Type 1 Subtype B Ancestral Envelope Protein Is Functional and Elicits Neutralizing Antibodies in Rabbits Similar to Those Elicited by a Circulating Subtype B Envelope J. Virol., September 1, 2005; 79(17): 11214 - 11224. [Abstract] [Full Text] [PDF]
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J. E. Aagaard, R. G. Olmstead, J. H. Willis, and P. C. Phillips Duplication of floral regulatory genes in the Lamiales Am. J. Botany, August 1, 2005; 92(8): 1284 - 1293. [Abstract] [Full Text] [PDF]
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M. Kennedy, B. R. Holland, R. D. Gray, and H. G. Spencer Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks Syst Biol, August 1, 2005; 54(4): 620 - 633. [Abstract] [Full Text] [PDF]
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E. J. Edwards, R. Nyffeler, and M. J. Donoghue Basal cactus phylogeny: implications of Pereskia (Cactaceae) paraphyly for the transition to the cactus life form Am. J. Botany, July 1, 2005; 92(7): 1177 - 1188. [Abstract] [Full Text] [PDF]
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Y.-x. Luan, J. M. Mallatt, R.-d. Xie, Y.-m. Yang, and W.-y. Yin The Phylogenetic Positions of Three Basal-Hexapod Groups (Protura, Diplura, and Collembola) Based on Ribosomal RNA Gene Sequences Mol. Biol. Evol., July 1, 2005; 22(7): 1579 - 1592. [Abstract] [Full Text] [PDF]
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P. Lopez-Sanchez, J. C. Costas, and H. F. Naveira Paleogenomic Record of the Extinction of Human Endogenous Retrovirus ERV9 J. Virol., June 1, 2005; 79(11): 6997 - 7004. [Abstract] [Full Text] [PDF]
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