Description

Simulates gene trees under a phylogenetic network model.

Usage

simGTinNetwork network_ident numGTs [-a taxonMap] [-ms msPath]

network_ident

The name of the model phylogenetic network.

mandatory

numGTs

The number of gene trees to simulate.

mandatory

-a taxonMap

Gene tree / species tree taxa association.

optional

-ms msPath

The path of MS program installed in local directory. Without specifying msPath, only gene tree topologies are simulated.

optional


Example

#NEXUS
BEGIN NETWORKS;
Network net = ((A:2,((B:1,C:1):1)X#H1:0::0.3):1,(D:2,X#H1:0::0.7):1);
END;

BEGIN PHYLONET;
simGTinNetwork net 4 -ms "/Users/abc/tools/msdir/ms";
END;

Output

simGTinNetwork net 10 -ms "/Users/dw20/tools/msdir/ms"
ms 4 10 -T -I 4 1 1 1 1 -ej 0.5 2 1 -es 1.0 1 0.3 -ej 1.0 4 1 -ej 1.0 3 5 -ej 1.5 1 5
 
(C:3.35844636,(A:3.116672278,(B:2.789166928,D:2.789166928):0.32750535):0.241774082);
(D:3.720724344,(A:3.405322552,(C:1.535019994,B:1.535019994):1.870302558):0.315401792);
(A:4.14922905,(D:2.299737216,(C:1.864839912,B:1.864839912):0.434897304):1.849491834);
(D:3.734062194,(A:2.87092328,(C:1.911041498,B:1.911041498):0.959881782):0.863138914);
  • PhyloNet command
  • MS command (Hudson, R. R. (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337-8.)
  • Simulated gene trees

See Also

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