Versions Compared

Old Version 1

changes.mady.by.user Robert Barnett

Saved on

compared with

New Version Current

changes.mady.by.user Ellie Wen

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Migrated to Confluence 5.3

Description

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

Usage

Code Block
langhtml


cmpnetssimGTinNetwork network_ident1ident network_ident2numGTs [-m [tree|tri|clustera taxonMap] [result output file-ms msPath]

network_ident1ident

The name of the first model phylogenetic network.

mandatory

network_ident2 numGTs

The name of the second networknumber of gene trees to simulate.

mandatory

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ebd24b8b-1a01-4496-934b-4836470c5a5e"><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

...

-a taxonMap

Gene tree / species tree taxa association.

optional

-ms msPath

The path of MS program installed in local directory. Without specifying msPath, only gene tree topologies are simulated.

optional


Example

Code Block
langhtml

#NEXUS

BEGIN NETWORKS;

Network net1net = ((aA:2,(b,(c)x#1)),((d,x#1),e));
Network net2 = ((((a, (c)x#1), d), (b, x)), e);
(B:1,C:1):1)X#H1:0::0.3):1,(D:2,X#H1:0::0.7):1);
END;


BEGIN PHYLONET;

CmpnetssimGTinNetwork net1net net24 -m clusterms "/Users/abc/tools/msdir/ms";

END;

Command References

Output

Code Block
langhtml
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 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.

See Also