Generates DNA sequences based on Markov model techniques for matched sequences. This can be generalized to several sequences. The sequences (taxa) are then arranged in an evolutionary tree (phylogenetic tree) depicting how taxa diverge from their common ancestors. This gives the tests and estimation methods for the parameters of different models. Standard phylogenetic methods assume stationarity, homogeneity and reversibility for the Markov processes, and often impose further restrictions on the parameters.

Author | Faisal Ababneh, John Robinson, Lars S Jermiin and Hasinur Rahaman Khan |

Date of publication | 2016-03-24 23:32:09 |

Maintainer | Hasinur Rahaman Khan <hasinurkhan@gmail.com> |

License | GPL-2 |

Version | 1.0 |

**artomat:** Transforming 4^K Array to m \times K Matrix

**Distance:** Paralinear Distances

**DNAseqtest-package:** Generating and Testing DNA Sequences

**Fmatrix:** Joint Distribution for Two Matched Sequences

**gn:** Joint Distribution for K Matched Sequences

**gn2:** Joint Distribution for K Matched Sequences (2)

**gn3sim:** Generating Random DNA Samples Using the Rambaut and Grassly...

**likelihood:** Negative Log Likelihood Ratio

**Ntml:** Generating Samples from a Multinomial Distribution

**Pt:** Transition Probability Function

**simapp:** Generating Random DNA Samples Using Approximation Method

**simemb:** Generating Random DNA Samples Using Embedded Markov Chain

**Smatrix:** Symmetric Matrix S

**TEST2:** Test for Symmetry of Matched DNA Sequences

**TEST3:** Overall Test for Marginal Symmetry

DNAseqtest

DNAseqtest/NAMESPACE

DNAseqtest/R

DNAseqtest/R/TEST3.R
DNAseqtest/R/Ntml.R
DNAseqtest/R/Smatrix.R
DNAseqtest/R/simemb.R
DNAseqtest/R/gn.R
DNAseqtest/R/TEST2.R
DNAseqtest/R/Distance.R
DNAseqtest/R/Fmatrix.R
DNAseqtest/R/gn3sim.R
DNAseqtest/R/likelihood.R
DNAseqtest/R/Pt.R
DNAseqtest/R/simapp.R
DNAseqtest/R/gn2.R
DNAseqtest/R/artomat.R
DNAseqtest/MD5

DNAseqtest/DESCRIPTION

DNAseqtest/man

DNAseqtest/man/artomat.Rd
DNAseqtest/man/Distance.Rd
DNAseqtest/man/simemb.Rd
DNAseqtest/man/likelihood.Rd
DNAseqtest/man/gn2.Rd
DNAseqtest/man/Pt.Rd
DNAseqtest/man/gn.Rd
DNAseqtest/man/Ntml.Rd
DNAseqtest/man/gn3sim.Rd
DNAseqtest/man/Smatrix.Rd
DNAseqtest/man/Fmatrix.Rd
DNAseqtest/man/DNAseqtest-package.Rd
DNAseqtest/man/TEST3.Rd
DNAseqtest/man/simapp.Rd
DNAseqtest/man/TEST2.Rd
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.