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InferNetwork_parsimonyMP (gene_tree_ident1 [, gene_tree_ident2...]) numReticulations [-a taxa map] [-b threshold] [-s startingNetwork] [-n numNetReturned]  [-m maxNetExamined] [-d maxDiameter] [-h {s1 [,s2...]}] [-w (w1,w2,w3,w4)] [-f maxFailure] [-x numRuns] [-pl numProcessors] [-di] [result output file]

#NEXUS

BEGIN TREES;

Tree geneTree1 = (C,((B,D),A));
Tree geneTree2 = (B,(D,(C,A)));
Tree geneTree3 = (D,(B,(C,A)));
Tree geneTree4 = (D,(B,(C,A)));

END;


BEGIN PHYLONET;

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

END;

#NEXUS

BEGIN TREES;

Tree geneTree1 = [&W 0.8] (C,((B,D),A));
Tree geneTree2 = [&W 0.2] (B,(D,(C,A)));
Tree geneTree3 = [&W 0.7] (D,(B,(C,A)));
Tree geneTree4 = [&W 0.3] (D,(B,(C,A)));

END;


BEGIN PHYLONET;

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

END;