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Refines and root gene trees with respect to a rooted binary species tree under MDC criterion. The input gene trees must be specified in the rich newick format Rich Newick Format. Gene trees must be rooted. Gene losses are allowed. The generated output trees will also be generated in the rich newick format. Multiple species trees may be specified in which case the tool will run in batch mode with one execution of each species tree and set of gene trees.

Usage

Process_GT {species_tree_ident1 [, species_tree_ident2...]} {gene_tree_ident1 [, gene_tree_ident2...]} [-u] [-b threshold] [-a taxa map] [result output file]

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Examples

#NEXUS

BEGIN TREES;

Tree speceiesTree = ((((a:1,b:2),c:3),d:4),e:5);
Tree geneTree1 = (((a:1,b:2,c:3),d:4),e:5);
END;


BEGIN PHYLONET;

ProcessGT {speceiesTree, speceiesTree} {geneTree1};

END;

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