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DeepCoalCount_tree {species_tree_ident1 [, species_tree_ident2...]} (gene_tree_ident1 [, gene_tree_ident2...]) [-u] [-b threshold] [-a taxa map] [result output fileoutputFile]
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species_tree_ident1 [, species_tree_ident2...] | Comma delimited set of species tree identifiers. | mandatory |
gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited list of gene tree identifiers. See details. | mandatory |
-u | Gene trees should be treated as unrooted. | optional |
-b threshold | Gene tree 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 |
result output file outputFile | Optional file destination for command output. | optional |
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