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Simulates gene trees under the phylogenetic network model in Yu et al. (see Command References).

Usage

Code Block
langhtml

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 tree, tri, or cluster.

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

Code Block
langhtml
#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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