PhyloCTMC distribution

PhyloCTMC(TimeTree tree, Number mu, Double[] freq, Double[][] Q, Double[] siteRates, Double[] branchRates, Integer L, SequenceType dataType, SimpleAlignment root)

The phylogenetic continuous-time Markov chain distribution. A sequence is simulated for every leaf node, and every direct ancestor node with an id.(The sampling distribution that the phylogenetic likelihood is derived from.)

Parameters

TimeTree tree - the time tree.
Number mu - (optional) the clock rate. Default value is 1.0.
Double[] freq - (optional) the root probabilities. Optional parameter. If not specified then first row of e^{100*Q) is used.
Double[][] Q - the instantaneous rate matrix.
Double[] siteRates - (optional) a rate for each site in the alignment. Site rates are assumed to be 1.0 otherwise.
Double[] branchRates - (optional) a rate for each branch in the tree. Original branch rates are used if rates not given. Branch rates are assumed to be 1.0 otherwise.
Integer L - (optional) length of the alignment
SequenceType dataType - (optional) the data type used for simulations, default to nucleotide
SimpleAlignment root - (optional) root sequence, defaults to root sequence generated from equilibrium frequencies.

Return type

Alignment

Examples

gtrGammaCoalescent.lphy
errorModel1.lphy

Reference

Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of molecular evolution, 17(6), 368-376.https://doi.org/10.1007/BF01734359

PhyloCTMC(TimeTree tree, Number mu, Double[] freq, SiteModel siteModel, Double[] branchRates, Integer L, SequenceType dataType)