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<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ef9efdf41d82780e-604218d6-4a5e4427-b546af04-d91141709c59baaa195260d2"><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="f30435d519614165-0fa8586b-4e774194-9eb1abc8-6e44b7e5d73b781d1691b3fc"><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 |
By default, it is assumed that gene trees are rooted. In this case, the method refines the gene trees with respect to the species tree. If the gene trees are unrooted, users can
use option -u. In this case, the method not only refines and but also roots gene trees.
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