Computer applications in the biosciences · 1997 · 1.7K citations · 27 references
Life SciencesBiologyEvolutionary BiologyEvolutionary TheoryMolecular EvolutionPhylogeneticsBootstrapping In PhylogeneticsPhylogenetic AnalysisPhylogenetic InferencePhylogenetic Sequence AnalysisPhylogenetic Tree ReconstructionBootstrap AnalysisBootstrap ReplicatesBootstrap ResamplingNucleotide Evolution ModelsParametric BootstrapParametric Bootstrap TestingRate HeterogeneitySite-specific Evolutionary Models
Seq‑Gen simulates nucleotide sequence evolution along phylogenies using standard substitution models. It implements a range of molecular evolution models—including a general reversible model—and accepts user‑specified nucleotide frequencies, rate heterogeneity, and multiple trees to generate datasets. The tool enables rapid generation of large replicate simulation sets for parametric bootstrap testing of phylogenetic hypotheses. Seq‑Gen is freely available from the authors’ website (via WWW or FTP) and includes source code, a manual, example files, and a Macintosh version.
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.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.
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