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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 |
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-ms msPath | The path of ms installed in local directory. Without specifying msPath, only gene tree topologies are simulated. | optional |
Examples
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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 1net 210 .5 3 -ms "/Users/abc/tools/msdir/ms"; END; |
Command References
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