Simulation suite

Compilation of scripts to simulate data on phylogenetic networks

I want to

• Simulate phylogenetic networks under a birth-death-hybridization model using SiPhyNetworks R package

  • Use scripts/simulate-networks.R
  • Dependencies:
    • R (version 4.1.2 or higher)
    • SiPhyNetwork:

    install.packages("devtools")
    devtools::install_github("jjustison/SiPhyNetwork")
    

  • Input parameters:
    • N: number of networks to simulate
    • lambda: speciation rate
    • mu: extinction rate
    • nu: hybridization rate
    • hybprobs: 3d vector with frequencies of each of the three types of hybridizations (see here)
    • ntips: number of tips in the network
    • seed: random seed for reproducibility
  • Output:
    • N output files each with a simulated network in parenthetical format. Note that branches on the network depend on the units of the rates
    • text file with parameters selected for reproducibility

• Simulate gene trees on a given species network (or tree) under the multispecies coalescent using ms

  • Use scripts/simulate-gene-trees-ms.jl
  • Dependencies:
    • ms:
      • Download ms.tar.gz here
      • Move the folder to wherever you want it
      • Untar tar -xvf ms.tar.gz to create the msdir folder
      • Inside msdir, compile

      gcc -o ms ms.c streec.c rand2.c -lm
      

      Note that we use rand2.c so that the number generator used is rand(), not drand48() which is supposed to be inferior.
      • Copy the ms executable in /usr/local/bin or somewhere in your PATH, or add the path to it to PATH
    • Julia (version 1.8 or higher)
    • PhyloNetworks package, see here. In Julia:

    ] add PhyloNetworks

  • Input:
    • msnet: text file with the network in ms format, see ms docs. Branch lengths are assumed to be in coalescent units. This file containts the -ej and -es events
    • net: text file with the network in parenthetical format.
    • numalleles: number of alleles per taxon. This script assumes all taxa have the same number of alleles, but see notes in the jl script).
    • numgt: number of gene trees to simulate
  • Output:
    • treefile: text file with simulated gene trees (one per line) in parenthetical format.