synDss: Recombination detection using synonymous distances
Version 0.0-1

Based on the sliding windows methods of TOPALi, this package allows for detection of recombination using synonymous distnaces, which avoids false positives due to localized convergent evolution

AuthorPeter Chi, Vladimir Minin
Date of publication2013-12-12 22:18:52
MaintainerPeter Chi <pchi@calpoly.edu>
LicenseGPL-3
Version0.0-1
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("synDss", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

conv.evol: Simulate convergent evolution
fasta.to.alignment: Internal function, used by sim.codon.
make.dat: Internal function, used by sim.codon.
nuc.to.codon: Convert nucleotide sequence alignment to a codon sequence...
read.phylosim: Convert alignment to be readable for synonymous distance...
sim.codon: Simulate a codon sequence alignment
synDss-package: synDss: Recombination detection with synonymous distances
See all...

All man pages Function index File listing

Man pages

calc.Dss: Calculate the Dss statistic
calc.Dss.syn: Calculate the Dss statistic using synonymous distances
calc.null.pboot: Calculate the null distribution of the Dss statistic using...
calc.null.pboot.syn: Calculate the null distribution of the Synonymous Dss...
conv.evol: Simulate convergent evolution
fasta.to.alignment: Internal function, used by sim.codon.
make.dat: Internal function, used by sim.codon.
make.mj.align: Convert alignment to be readable for synonymous distance...
nuc.to.codon: Convert nucleotide sequence alignment to a codon sequence...
optim.phylo.ls.all: Least squares phylogenetic estimation with an exhaustive...
paml.codeml: Estimate parameters from the M3 codon substitution model
read.phylosim: Convert alignment to be readable for synonymous distance...
sim.codon: Simulate a codon sequence alignment
synDss-package: synDss: Recombination detection with synonymous distances

Functions

calc.Dss Man page Source code
calc.Dss.syn Man page Source code
calc.null.pboot Man page Source code
calc.null.pboot.syn Man page Source code
conv.evol Man page Source code
fasta.to.alignment Man page Source code
make.dat Man page Source code
make.mj.align Man page Source code
nuc.to.codon Man page Source code
optim.phylo.ls.all Man page Source code
paml.codeml Man page Source code
read.phylosim Man page Source code
sim.codon Man page Source code
synDss Man page
synDss-package Man page

Files

DESCRIPTION
NAMESPACE
R
R/calc.Dss.R
R/calc.Dss.syn.R
R/calc.null.pboot.R
R/calc.null.pboot.syn.R
R/conv.evol.R
R/fasta.to.alignment.R
R/make.dat.R
R/make.mj.align.R
R/nuc.to.codon.R
R/optim.phylo.ls.all.R
R/paml.codeml.R
R/read.phylosim.R
R/sim.codon.R
R/synDss-internal.R
doc
doc/sal18.pdf
doc/tutorial.Rnw
inst
inst/paml
inst/paml/template.ctl
inst/paml/template.dat
inst/seqdata
inst/seqdata/Salmonella_fimH_aligned-18alleles.txt
inst/seqdata/set7_env.fasta
inst/seqdata/set7_pol.fasta
man
man/calc.Dss.Rd
man/calc.Dss.syn.Rd
man/calc.null.pboot.Rd
man/calc.null.pboot.syn.Rd
man/conv.evol.Rd
man/fasta.to.alignment.Rd
man/make.dat.Rd
man/make.mj.align.Rd
man/nuc.to.codon.Rd
man/optim.phylo.ls.all.Rd
man/paml.codeml.Rd
man/read.phylosim.Rd
man/sim.codon.Rd
man/synDss-package.Rd
synDss documentation built on May 21, 2017, 1:32 a.m.

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