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Code Block
langhtml
InferNetwork_MPL geneTreeList numReticulations [-a taxa map] [-b threshold] [-s startingNetwork] [-fs] [-n numNetReturned] [-h {s1 [,s2...]}] [-w (w1,...,w7)] [-x numRuns] [-m maxNetExamined] [-md moveDiameter] [-rd reticulationDiameter] [-f maxFailure] [-o] [-po] [-p (rel,abs)] [-r maxRounds] [-t maxTryPerBr] [-i improveThreshold] [-l maxBL] [-pl numProcessors] [-di] [result output fileresultOutputFile]

geneTreeList

Comma delimited list of gene tree identifiers or comma delimited list of sets of gene tree identifiers. See details.

mandatory

numReticulations

Maximum number of reticulations to added.

mandatory

-b threshold

Gene trees bootstrap threshold. Edges in the gene trees that have support lower than threshold will be contracted.

optional

-a taxa map

Gene tree / species tree taxa association.

optional

-s startingNetwork

Specify the network to start search. Default value is the optimal MDC tree.

optional
-fsFix the start tree for search. If specified and give a start tree (-s), the search will fix the topology of the start tree.optional

-n numNetReturned

Number of optimal networks to return. Default value is 5.

optional
-h {s1 [, s2...]}

A set of specified hybrid species.

optional
-w (w1, ..., w7)

The weights of operations for network arrangement during the network search. Default value is (0.1,0.1,0.15,0.55,0.15,0.15,2.8).

optional

-x numRuns 

The number of runs of the search. Default value is 10.

optional

-m maxNetExamined

Maximum number of network topologies to examined. Default value is infinity.

optional
-md moveDiameterMaximum diameter to make an arrangement during network search. Default value is infinity.optional

-rd reticulationDiameter

Maximum diameter for a reticulation event (the distance between two parents of a reticulation node). Default value is infinity.

optional
-f maxFailureMaximum consecutive number of failures for hill climbing. Default value is 100.optional
-oIf specified, during the search, for every proposed species network, its branch lengths and inheritance probabilities will be optimized to compute its likelihood. Default value is false.optional
-poIf specified, after the search the returned species networks will be optimized for their branch lengths and inheritance probabilities under full likelihood. Default value is false.optional

-p (rel, abs)

The original stopping criterion of Brent’s algorithm. Default value is (0.01, 0.001).

optional

-r maxRound

Maximum number of rounds to optimize branch lengths for a network topology. Default value is 100.

optional

-t maxTryPerBr

Maximum number of trial per branch in one round to optimize branch lengths for a network topology. Default value is 100.

optional

-i improveThreshold

Minimum threshold of improvement to continue the next round of optimization of branch lengths. Default value is 0.001.

optional

-l maxBL

Maximum branch lengths considered. Default value is 6.

optional

-pl numProcessors 

Number of processors if you want the computation to be done in parallel. Default value is 1.

optional
-diOutput the Rich Newick string of the inferred network that can be read by Dendroscope .optional

result output fileresultOutputFile

Optional file destination for command output.

optional

...

Code Block
langhtml
#NEXUS

BEGIN TREES;

Tree geneTree1 gt0= ((C(a:2.299,((B,D),A)),Ee:1.329,f:1.329):0.77,(c:1.684,(b:1.232,d:1.232):0.451):0.416):0.2);
Tree geneTree2 gt1= (Ba:2.085,(D,(C,(A,E)))((e:1.376,f:1.376):0.696,(d:1.487,(b:1.241,c:1.241):0.246):0.585):0.013);
Tree geneTree3 gt2= (D,(B,((C,E),A)))((c:0.52,d:0.52):1.243,(e:1.403,f:1.403):0.36):1.025,(a:1.863,b:1.863):0.925);
Tree geneTree4 gt3= (Da:2.82,((B,E),(C,A)));

END;


BEGIN PHYLONET;

InferNetwork_MPL (geneTree1,geneTree2,geneTree3,geneTree4) 1;

END;
Code Block
langhtml
#NEXUS

BEGIN TREES;

Tree geneTree1 = [&W 0.9] ((C,((B,D),A)),E);
Tree geneTree2 = [&W 0.1] (B,(D,(C,(A,E))));
Tree geneTree3 = [&W 0.6] (D,(B,((C,E),A)));
Tree geneTree4 = [&W 0.4] (D,((B,E),(C,A))(b:1.051,(c:0.86,d:0.86):0.19):1.357,(e:1.365,f:1.365):1.043):0.412);
Tree gt4=((e:1.3,f:1.3):0.994,(a:1.869,(b:1.255,(c:0.849,d:0.849):0.405):0.615):0.425);
Tree gt5=(a:2.46,((b:1.077,c:1.077):0.857,(f:1.141,(d:0.505,e:0.505):0.636):0.793):0.526);
Tree gt6=(a:2.025,((b:1.111,c:1.111):0.416,(f:1.304,(d:0.727,e:0.727):0.577):0.223):0.498);
Tree gt7=((d:1.526,(e:1.415,f:1.415):0.111):0.982,(a:2.188,(b:1.532,c:1.532):0.656):0.32);
Tree gt8=(a:2.234,((b:1.057,c:1.057):0.766,(f:1.301,(d:0.849,e:0.849):0.452):0.522):0.411);
Tree gt9=((e:1.644,(b:1.361,(c:0.503,d:0.503):0.858):0.283):0.787,(a:2.226,f:2.226):0.205);
Tree gt10=(a:2.917,((e:1.683,(c:0.961,d:0.961):0.722):0.886,(b:1.779,f:1.779):0.79):0.348);
Tree gt11=(a:2.391,((b:1.041,(c:0.602,d:0.602):0.439):0.516,(e:1.164,f:1.164):0.393):0.834);
Tree gt12=((b:1.21,c:1.21):1.622,(a:2.443,(f:1.804,(d:0.583,e:0.583):1.221):0.639):0.389);
Tree gt13=(a:2.047,((b:1.025,c:1.025):0.519,(f:1.295,(d:0.738,e:0.738):0.556):0.249):0.503);
Tree gt14=(a:2.58,((d:0.919,e:0.919):0.834,(f:1.503,(b:1.228,c:1.228):0.275):0.251):0.827);
Tree gt15=((f:1.267,(d:0.871,e:0.871):0.396):1.67,(a:2.181,(b:1.362,c:1.362):0.819):0.756);
Tree gt16=(a:3.016,(b:1.892,(c:1.816,(f:1.479,(d:0.812,e:0.812):0.667):0.337):0.076):1.124);
Tree gt17=((f:1.186,(d:0.721,e:0.721):0.465):1.822,(a:2.031,(b:1.13,c:1.13):0.902):0.977);
Tree gt18=((c:1.51,(f:1.166,(d:0.521,e:0.521):0.645):0.345):1.218,(a:2.073,b:2.073):0.655);
Tree gt19=(a:2.329,((b:1.354,c:1.354):0.467,(f:1.392,(d:0.955,e:0.955):0.437):0.429):0.508);
Tree gt20=(a:3.31,((e:1.083,f:1.083):2.08,(b:1.923,(c:0.538,d:0.538):1.385):1.241):0.146);
Tree gt21=((e:1.271,f:1.271):0.969,(a:1.687,(c:1.131,(b:1.012,d:1.012):0.119):0.556):0.554);
Tree gt22=(c:4.001,((f:1.146,(d:0.896,e:0.896):0.25):1.216,(a:1.542,b:1.542):0.82):1.639);
Tree gt23=((e:1.147,f:1.147):1.081,(a:1.658,(b:1.08,(c:0.611,d:0.611):0.469):0.578):0.569);
Tree gt24=(f:3.318,(a:2.154,((b:1.086,c:1.086):0.78,(d:1.105,e:1.105):0.761):0.287):1.164);
Tree gt25=(a:2.153,((b:1.031,c:1.031):0.598,(f:1.469,(d:0.638,e:0.638):0.831):0.16):0.524);
Tree gt26=(a:4.225,((b:1.1,c:1.1):0.808,(f:1.365,(d:0.7,e:0.7):0.665):0.543):2.316);
Tree gt27=((a:1.756,b:1.756):1.852,(c:2.162,(d:1.829,(e:1.149,f:1.149):0.68):0.333):1.446);
Tree gt28=(a:3.675,((f:1.002,(d:0.652,e:0.652):0.35):0.898,(b:1.342,c:1.342):0.558):1.775);
Tree gt29=((b:1.343,c:1.343):0.843,(a:2.014,(e:1.686,(d:1.523,f:1.523):0.163):0.328):0.171);
Tree gt30=(a:2.171,((b:1.223,c:1.223):0.631,(f:1.63,(d:0.528,e:0.528):1.101):0.224):0.317);
Tree gt31=(a:2.022,((b:1.134,c:1.134):0.877,(f:1.147,(d:0.891,e:0.891):0.256):0.864):0.011);
Tree gt32=(d:2.582,(a:2.139,((b:1.062,c:1.062):0.667,(e:1.105,f:1.105):0.624):0.41):0.443);
Tree gt33=((b:1.112,c:1.112):2.227,(a:2.025,(d:1.491,(e:1.163,f:1.163):0.328):0.534):1.315);
Tree gt34=((f:1.411,(d:0.744,e:0.744):0.667):1.881,(a:1.84,(b:1.241,c:1.241):0.599):1.452);
Tree gt35=(a:2.415,((b:1.132,d:1.132):1.098,(e:1.571,(c:1.517,f:1.517):0.055):0.659):0.185);
Tree gt36=(a:2.426,((c:1.506,(d:0.846,e:0.846):0.66):0.281,(b:1.677,f:1.677):0.111):0.638);
Tree gt37=((c:1.617,(f:1.018,(d:0.565,e:0.565):0.453):0.598):0.624,(a:1.735,b:1.735):0.506);
Tree gt38=(a:3.036,((e:1.187,f:1.187):1.057,(c:1.497,(b:1.263,d:1.263):0.234):0.747):0.793);
Tree gt39=(a:2.492,((b:1.262,(c:0.807,d:0.807):0.455):0.725,(e:1.412,f:1.412):0.574):0.505);
Tree gt40=(a:3.378,((e:1.249,(d:1.116,f:1.116):0.132):0.311,(b:1.344,c:1.344):0.215):1.819);
Tree gt41=(a:2.082,(c:1.812,((d:0.542,e:0.542):1.268,(b:1.571,f:1.571):0.239):0.0020):0.27);
Tree gt42=((e:1.845,f:1.845):0.27,(a:1.965,(b:1.187,(c:0.715,d:0.715):0.471):0.778):0.15);
Tree gt43=(a:2.845,((f:1.296,(d:0.605,e:0.605):0.691):0.442,(b:1.501,c:1.501):0.237):1.107);
Tree gt44=(a:2.504,(b:2.482,(e:1.809,(f:1.565,(c:1.129,d:1.129):0.436):0.244):0.673):0.021);
Tree gt45=(a:2.758,((e:1.214,(d:1.008,f:1.008):0.206):0.433,(b:1.499,c:1.499):0.148):1.111);
Tree gt46=((f:1.165,(d:0.708,e:0.708):0.457):1.122,(a:1.873,(b:1.466,c:1.466):0.406):0.415);
Tree gt47=(a:2.406,((d:1.154,(e:1.117,f:1.117):0.037):1.104,(b:1.612,c:1.612):0.646):0.148);
Tree gt48=(a:2.155,(f:1.603,(e:1.55,(b:1.228,(c:0.504,d:0.504):0.724):0.322):0.053):0.552);
Tree gt49=(a:2.831,((e:1.492,f:1.492):0.176,(d:1.53,(b:1.401,c:1.401):0.13):0.138):1.163);

END;


BEGIN PHYLONET;

InferNetwork_MPL (geneTree1,geneTree2,geneTree3,geneTree4all) 1 -o2;

END;

 


Command References

See Also