synDss: Recombination detection using synonymous distances

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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

Author
Peter Chi, Vladimir Minin
Date of publication
2013-12-12 22:18:52
Maintainer
Peter Chi <pchi@calpoly.edu>
License
GPL-3
Version
0.0-1

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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

Files in this package

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