/simulation-suite

Myriad of scripts to simulate data in phylogenetics

Primary LanguageC++MIT LicenseMIT

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: 
      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.