Seq-Gen swMATH ID: 8310 Software Authors: Andrew Rambaut; Nick C. Grassly Description: 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. Homepage: https://academic.oup.com/bioinformatics/article/13/3/235/423110 Related Software: fastDNAml; PHYLIP; BIONJ; RAxML; MrBayes; FastTree; ASTRAL-II; BEAST; STEM-hy; phangorn; ape; MODELTEST; R; Scoredist; r8s; TRANSFAC; MEME; BioProspector; GenRGenS; HyDe Cited in: 26 Publications all top 5 Cited by 62 Authors 2 Kubatko, Laura Salter 2 Nye, Tom M. W. 2 Richards, Andrew 2 Suchard, Marc A. 1 Ababneh, Faisal 1 Allen, Chabrielle 1 Benedict, Travis 1 Biggs, Patrick J. 1 Bloomquist, Erik W. 1 Boulanger, Frédéric 1 Carbone, Alessandra 1 Cox, Murray P. 1 Darlu, Pierre 1 Deeks, Steven G. 1 DeGiorgio, Michael 1 Dehmer, Matthias 1 Desper, Richard 1 Dib, Linda 1 Dulworth, Peter 1 Elias, Isaac 1 Elworth, Ryan A. Leo 1 Emmert-Streib, Frank 1 Fearnhead, Paul 1 French, Nigel P. 1 Futschik, Andreas 1 Gach, Florian 1 Gascuel, Olivier 1 Gesell, Tanja 1 Gilks, Walter R. 1 Górecki, Paweł 1 Guénoche, Alain 1 Holmes, Susan P. 1 Hurn, Merrilee A. 1 Huzurbazar, Snehalata 1 Ionescu, Tudor B. 1 Jermiin, Lars S. 1 Jhwueng, Dwueng-Chwuan 1 Kitchen, Christina M. R. 1 Kroll, Jing 1 Kuritzkes, Daniel R. 1 Lagergren, Jens 1 Levy, Dan 1 Liò, Pietro 1 Liu, Liang 1 Loza-Reyes, E. 1 Ma, Bin 1 Mihaescu, Radu 1 Minin, Vladimir N. 1 Mykowiecka, Agnieszka 1 Nakhleh, Luay 1 O’Meara, Brian C. 1 Pachter, Lior 1 Paeng, Seong-Hun 1 Paradis, Emmanuel 1 Park, Chunjae 1 Polaillon, Géraldine 1 Prangle, Dennis 1 Radice, Rosalba 1 Robinson, John 1 Rosenberg, Noah A. 1 Xin, Lei 1 Zhang, Kaizhong all top 5 Cited in 17 Serials 3 Statistical Applications in Genetics and Molecular Biology 2 Theoretical Computer Science 2 Theoretical Population Biology 2 Journal of Classification 2 Computational Statistics and Data Analysis 1 Journal of Mathematical Biology 1 Bulletin of Mathematical Biology 1 The Annals of Statistics 1 Applied Mathematics and Computation 1 Statistical Science 1 Algorithmica 1 Journal of Combinatorial Optimization 1 Australian & New Zealand Journal of Statistics 1 Communications of the Korean Mathematical Society 1 JMMA. Journal of Mathematical Modelling and Algorithms 1 Journal of Theoretical Biology 1 Use R! all top 5 Cited in 7 Fields 20 Biology and other natural sciences (92-XX) 11 Statistics (62-XX) 5 Numerical analysis (65-XX) 3 Probability theory and stochastic processes (60-XX) 3 Computer science (68-XX) 2 Combinatorics (05-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year