DNAseqtest: Generating and Testing DNA Sequences

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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

View on CRAN

Man pages

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

Files in this package

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