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Infer the species tree from unrooted gene trees using MDC criterion. The input gene trees must be specified in the rich newick format Rich Newick Format. Gene trees must be unrooted. The generated output trees will also be generated in the rich newick format.
Usage
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Infer_ST_MDC_UR {(gene_tree_ident1 [, gene_tree_ident2...]}) [-e proportion] [-x] [-b threshold] [-a taxa map] [-ur] [-t time] [result output file] |
gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited set list of gene tree identifiers. See details. | mandatory |
-e proportion | Get optimal and sub-optimal trees. | optional |
-x | Use all clusters in generation. | optional |
-b threshold | Specifies 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 |
-ur | Allow non-binary species tree generation. | optional |
-t time | Limit search time to time minutes. | optional |
result output file | Optional file destination for command output. | optional |
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Examples
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#NEXUS
BEGIN NETWORKS;
Network g1 = ((((a:5,b:5):4,c:9):3,d:12):3,e:15);
Network g2 = ((a:6,b:6):11,((c:12,e:12):2,d:14):3);
Network g3 = ((a:8,c:8):7,((b:14,e:14):1,d:15));
END;
BEGIN PHYLONET;
Infer_ST_MDC_UR (g1, g2, g3);
END
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#NEXUS BEGIN NETWORKS; Network g1 = ((((a1::.5,b1::.5)::.5,c::.5)::.5,d::.5)::.5,e::.5)::.5; Network g2 = ((a2::.5,b2::.5)::.5,((c::.5,e::.5)::.5,d::.5)::.5)::.5; Network g3 = ((a::.5,c::.5)::.5,((b::.5,e::.5)::.5,d::.5)::.5)::.5; END; BEGIN PHYLONET; Infer_STInferST_MDC_UR (g1, g2, g3) -b .5 -e .2 -x -ur -t 1 -a <z:a1,a2,a; y:b1,b2,b; c:c; d:d; e:e>; END; |
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