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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. 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.
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<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="314128f2ba1102a3-50c838cd-41634ac3-aa7b86b6-74b69426117a41cb55f90778"><ac:plain-text-body><![CDATA[ | {species_tree_ident1 [, species_tree_ident2...]} | Comma delimited set of species tree identifiers. | mandatory | ]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="d2410b1b0f326dee-131f5aee-411f4f03-9f91a289-323f9ccf979e698d182c7af4"><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 | Treat gene trees as unrooted. | optional | ||
-b threshold | Specifies bootstrap threshold. | optional | ||
-a taxa map | Gene tree / species tree taxa association. | optional | ||
result output file | Optional file destination for command output. | optional |
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