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 17 articles )

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  1. Mykowiecka, Agnieszka; Górecki, Pawel: Bootstrapping algorithms for gene duplication and speciation events (2016)
  2. Paradis, Emmanuel: Analysis of phylogenetics and evolution with R (2012)
  3. Pratas, Frederico; Trancoso, Pedro; Sousa, Leonel; Stamatakis, Alexandros; Shi, Guochun; Kindratenko, Volodymyr: Fine-grain parallelism using multi-core, cell/BE, and GPU systems (2012)
  4. Brinkmeyer, Malte; Griebel, Thasso; Böcker, Sebastian: Polynomial supertree methods revisited (2011)
  5. Carbone, A.; Dib, L.: Co-evolution and information signals in biological sequences (2011)
  6. Nye, Tom M.W.: Principal components analysis in the space of phylogenetic trees (2011)
  7. Ionescu, Tudor B.; Polaillon, Géraldine; Boulanger, Frédéric: Minimum tree cost quartet puzzling (2010)
  8. Elias, Isaac; Lagergren, Jens: Fast neighbor joining (2009)
  9. Hayes, Matthew; Walenstein, Andrew; Lakhotia, Arun: Evaluation of malware phylogeny modelling systems using automated variant generation (2009)
  10. 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)
  11. Mihaescu, Radu; Levy, Dan; Pachter, Lior: Why neighbor-joining works (2009)
  12. Dehmer, Matthias; Emmert-Streib, Frank; Gesell, Tanja: A comparative analysis of multidimensional features of objects resembling sets of graphs (2008)
  13. Futschik, Andreas; Gach, Florian: On the inadmissibility of Watterson’s estimator (2008)
  14. Ma, Bin; Xin, Lei; Zhang, Kaizhong: A new quartet approach for reconstructing phylogenetic trees: Quartet joining method (2008)
  15. Minin, Vladimir N.; Suchard, Marc A.: Counting labeled transitions in continuous-time Markov models of evolution (2008)
  16. Ababneh, Faisal; Jermiin, Lars S.; Robinson, John: Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree (2006)
  17. Desper, Richard; Gascuel, Olivier: Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle (2002)