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Simulates gene trees under the phylogenetic network model in Yu et al. (see Command References).
Usage
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cmpnetssimGTinNetwork network_ident1 network_ident2 -m [tree|tri|cluster]T1 T2 γ n [result output file] |
T1 | Branch length | network_ident1 | The name of the first network. | mandatory | |||
T2 | Branch length | network_ident2 | The name of the second network. | mandatory | |||
γ | Probability value. | mandatory | |||||
n | Number of gene trees to simulate. | mandatory | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="10834fc8-8928-4077-a18b-fcdec5e6df28"><ac:plain-text-body><![CDATA[ | -m [tree|tri|cluster] | Characterization mode. One of | mandatory | ]]></ac:plain-text-body></ac:structured-macro> |
result output file | Optional file destination for command output. | optional |
For description of parameter, see Yu et al. in Command References.
Examples
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#NEXUS BEGIN NETWORKS; Network net1 = ((a,(b,(c)x#1)),((d,x#1),e)); Network net2 = ((((a, (c)x#1), d), (b, x)), e); END; BEGIN PHYLONET; CmpnetssimGTinNetwork net11 net22 -m cluster;.5 3 END; |
Command References
- Y. Yu, C. Than, J. Degnan, and L. Nakhleh. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology, 2010.
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