jrm
YaBB Newbies
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Posts: 2
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Hi Sergei;
Thanks for your response. I'm not quite clear on "codonCharacters is the length of the simulated alignment". I'm also unclear how to get the mixture of the mixture model. Wouldn't three rate matrices be required?
Below is what I have now.
Thanks again,
Joseph
VERBOSITY_LEVEL = 1; GTRRateMatrix = { { *, 0.00660730, 0.02214928, 0.00940329, 0.02401722,...} ... }; simFreqs = {{0.03509833,0.00660730,0.02214928,0.00940329...}}; Model GTR = (GTRRateMatrix, simFreqs); Tree fiveTaxaTree = ((1:1,2:1):1,3:2,4:2,5:2); GeneticCodeExclusions = "TAA,TAG,TGA"; codonCharacters = {{"A","C","G","T"} {"3",GeneticCodeExclusions,"",""}}; SetDialogPrompt("\nSave simulated data to"); fprintf(PROMPT_FOR_FILE, CLEAR_FILE); save_sims_to = LAST_FILE_PATH; IS_TREE_PRESENT_IN_DATA = 1; DATAFILE_TREE = Format(fiveTaxaTree,1,1); fprintf (stdout, "\n"); for (it=0; it<100; it=it+1) { DataSet sim = Simulate(fiveTaxaTree,simFreqs,codonCharacters,codons,0); DataSetFilter simFilter = CreateFilter(sim,1); fName = save_sims_to + "." + it; fprintf(fName,CLEAR_FILE,simFilter); /*SetParameter(STATUS_BAR_STATUS_STRING, "Replicate " + (it+1) + " of " + replicates + " generated", 0);*/ fprintf(stdout, "Replicate ", it+1, " of 100 generated"); }
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