DNAseqtest: Generating and Testing DNA Sequences
Version 1.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorFaisal Ababneh, John Robinson, Lars S Jermiin and Hasinur Rahaman Khan
Date of publication2016-03-24 23:32:09
MaintainerHasinur Rahaman Khan <hasinurkhan@gmail.com>
LicenseGPL-2
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DNAseqtest")

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

Functions

DNAseqtest Man page
DNAseqtest-package Man page
Distance Man page Source code
Fmatrix Man page Source code
Ntml Man page Source code
Pt Man page Source code
Smatrix Man page Source code
TEST2 Man page Source code
TEST3 Man page Source code
artomat Man page Source code
gn Man page Source code
gn2 Man page Source code
gn3sim Man page Source code
likelihood Man page Source code
simapp Man page Source code
simemb Man page Source code

Files

NAMESPACE
R
R/TEST3.R
R/Ntml.R
R/Smatrix.R
R/simemb.R
R/gn.R
R/TEST2.R
R/Distance.R
R/Fmatrix.R
R/gn3sim.R
R/likelihood.R
R/Pt.R
R/simapp.R
R/gn2.R
R/artomat.R
MD5
DESCRIPTION
man
man/artomat.Rd
man/Distance.Rd
man/simemb.Rd
man/likelihood.Rd
man/gn2.Rd
man/Pt.Rd
man/gn.Rd
man/Ntml.Rd
man/gn3sim.Rd
man/Smatrix.Rd
man/Fmatrix.Rd
man/DNAseqtest-package.Rd
man/TEST3.Rd
man/simapp.Rd
man/TEST2.Rd
DNAseqtest documentation built on May 19, 2017, 10:31 a.m.