...
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 MS program installed in local directory. Without specifying msPath, only gene tree topologies are simulated. | optional |
ExamplesExample
Code Block | ||
---|---|---|
| ||
#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 104 -ms "/Users/abc/tools/msdir/ms"; END; |
Output
Code Block | ||
---|---|---|
| ||
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