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 |
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