Seq-Gen

Seq-Gen. Sequence-Generator: An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid 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/Amino acid frequencies and other parameters of the model may be given and site-specific rate heterogeneity may 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. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution. The paper cited above contains details of the algorithm and a short discussion about the uses of Seq-Gen.


References in zbMATH (referenced in 30 articles )

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  1. Paeng, Seong-Hun; Park, Chunjae: Spectral method for reconstructing phylogenetic tree (2019)
  2. DeGiorgio, Michael; Rosenberg, Noah A.: Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure (2016)
  3. Mykowiecka, Agnieszka; Górecki, Pawel: Bootstrapping algorithms for gene duplication and speciation events (2016)
  4. Jhwueng, Dwueng-Chwuan; Huzurbazar, Snehalata; O’Meara, Brian C.; Liu, Liang: Investigating the performance of AIC in selecting phylogenetic models (2014)
  5. Loza-Reyes, E.; Hurn, M. A.; Robinson, A.: Classification of molecular sequence data using Bayesian phylogenetic mixture models (2014)
  6. Prangle, Dennis; Fearnhead, Paul; Cox, Murray P.; Biggs, Patrick J.; French, Nigel P.: Semi-automatic selection of summary statistics for ABC model choice (2014)
  7. Paradis, Emmanuel: Analysis of phylogenetics and evolution with R (2012)
  8. Pratas, Frederico; Trancoso, Pedro; Sousa, Leonel; Stamatakis, Alexandros; Shi, Guochun; Kindratenko, Volodymyr: Fine-grain parallelism using multi-core, cell/BE, and GPU systems (2012) ioport
  9. Radice, Rosalba: A Bayesian approach to modelling reticulation events with application to the ribosomal protein gene rps11 of flowering plants (2012)
  10. Brinkmeyer, Malte; Griebel, Thasso; Böcker, Sebastian: Polynomial supertree methods revisited (2011) ioport
  11. Carbone, A.; Dib, L.: Co-evolution and information signals in biological sequences (2011)
  12. Darlu, Pierre; Guénoche, Alain: TreeOfTrees method to evaluate the congruence between gene trees (2011)
  13. Gilks, Walter R.; Nye, Tom M. W.; Lio, Pietro: A variance-components model for distance-matrix phylogenetic reconstruction (2011)
  14. Nye, Tom M. W.: Principal components analysis in the space of phylogenetic trees (2011)
  15. Hao, Weilong: Orgconv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs (2010) ioport
  16. Ionescu, Tudor B.; Polaillon, Géraldine; Boulanger, Frédéric: Minimum tree cost quartet puzzling (2010)
  17. Elias, Isaac; Lagergren, Jens: Fast neighbor joining (2009)
  18. Hayes, Matthew; Walenstein, Andrew; Lakhotia, Arun: Evaluation of malware phylogeny modelling systems using automated variant generation (2009) ioport
  19. Kitchen, Christina M. R.; Kroll, Jing; Kuritzkes, Daniel R.; Bloomquist, Erik; Deeks, Steven G.; Suchard, Marc A.: Two-way Bayesian hierarchical phylogenetic models: an application to the co-evolution of gp120 and gp41 during and after enfuvirtide treatment (2009)
  20. Lemey, Philippe; Lott, Martin; Martin, Darren P.; Moulton, Vincent: Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning (2009) ioport

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