Description
Infers a species network(s) with a specified number of reticulation nodes under MDC criterion using parsimony-based method. The reticulation nodes in the inferred network will have inferred inheritance probabilities associated with them. To find the optimal network, steepest descent is used. The species network and gene trees must be specified in the Rich Newick Format. However, only topologies of them are used in the method.
The input gene trees can be gene tree distributions inferred from Bayesian methods like MrBayes. See the second example below.
Usage
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InferNetwork_MP (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]
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...
If users want to run the computation in parallel. Please specify the number of processors through option -pl.
Examples
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#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_MP (geneTree1,geneTree2,geneTree3,geneTree4) 1;
END;
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#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_MP (geneTree1,geneTree2,geneTree3,geneTree4) 1;
END;
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Command References
- Y. Yu, R.M. Barnett, and L. Nakhleh. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology, vol. 62, no. 5, pp. 738-751, 2013.
- Y. Yu, N. Ristic and L. Nakhleh. Fast algorithms and Heuristics for Phylogenomics under hybridization and incomplete lineage sorting. BMC Bioinformatics, vol. 14, no. Suppl 15, p. S6, 2013.
- Y. Yu, J. Dong, K. Liu, and L. Nakhleh, Probabilistic inference of reticulate evolutionary histories, Under Review.
See Also