/examples/example_V2.1.1.R

http://github.com/sbotond/phylosim · R · 16 lines · 5 code · 4 blank · 7 comment · 0 complexity · 7d210a350aad2977f4d6bf0c3c431570 MD5 · raw file 

    

  1. #!/usr/bin/env Rscript
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  3. ##
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  4. ## Example V2.1.1: Simulating substitutions under the JC69 model - compact example
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  5. ## See also the package vignette (vignette("PhyloSim",package="phylosim")).
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  6. ##
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  8. # load PhyloSim
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  9. library("phylosim")
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  11. # Run the simulation, display the alignment matrix: 
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  12. Simulate(PhyloSim(
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  13.         root.seq=sampleStates( NucleotideSequence(len=50,proc=list(list(JC69())) )),
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  14.         phylo=read.tree("data/3taxa.nwk")
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  15. ))$alignment
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