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Simulates gene trees under the a phylogenetic network model in Yu et al. (see Command References).
Usage
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simGTinNetwork T1network_ident T2numGTs γ n[-a taxonMap] [result output file-ms msPath] |
network_ident | The name of the model phylogenetic network | T1 | Branch length. | mandatory |
T2 | Branch length. | mandatory | ||
γ | Probability value. | mandatory | ||
numGTs | The number | n | Number of gene trees to simulate. | mandatory |
-a taxonMap | Gene tree / species tree taxa association | result output file | Optional file destination for command output. | optional |
For description of parameter, see Yu et al. in Command References.
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-ms msPath | The path of MS program installed in local directory. Without specifying msPath, only gene tree topologies are simulated. | optional |
Example
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#NEXUS#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
| Code Block | ||
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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); END; |
Command References
(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 treesY. Yu, C. Than, J. Degnan, and L. Nakhleh. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology, 2010.