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{species_tree_ident} | The input species tree identifier. | mandatory | ||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="62eccec1d813a896-059a1be1-42fe4b3e-a02f9baa-a96863fd3825438736d7d247"><ac:plain-text-body><![CDATA[ | {gene_tree_ident1 [, gene_tree_ident2...]} | Comma delimited set of gene tree identifiers. | mandatory | ]]></ac:plain-text-body></ac:structured-macro> |
-u | Prevent the trees from being refined and contracted. | optional | ||
-p prefix | Specifies a name prefix used to label internal nodes. If no prefix is specified, then the default prefix | optional | ||
-e | Present full solutions. | optional | ||
result output file | Optional file destination for command output. | optional |
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#NEXUS BEGIN TREES; Tree speceiesTree = ((e,(f,g):0.63:.70)::.80,((a:1,(b:2),c:3),d:4),e:5):0.5:.80):0.5:.67,d):0.6); Tree geneTree1 = (((a:1,b:2):0.5:.70,c:3),d:4),e:5);):0.6:.80,(d,((e,f):0.4:.70,g)::.70)::.80); Tree geneTree2 = ((e,(f,g):0.5:.70):0.6:.80,((a,b):0.5:.90,(c,d):0.5:.87):0.57:.72); END; BEGIN PHYLONET; ProcessGTRIATAHGT {speceiesTree, speceiesTree} {geneTree1, geneTree2}; END; |
Command Refernces
- L. Nakhleh, D. Ruths, and L.S. Wang. RIATA-HGT: A fast and accurate heuristic for reconstrucing horizontal gene transfer. In L. Wang, editor, Proceedings of the Eleventh International Computing and Combinatorics Conference (COCOON 05), pages 84–93, 2005. LNCS #3595.
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