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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. 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]
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<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="9ba46d4a685ad741-6e0cc898-4b5641f7-83b79e67-19ece086b24e8991d29b8cc7"><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> |
-e proportion | Get optimal and sub-optimal trees. | optional | ||
-x | Use all clusters in generation. | optional | ||
-b threshold | Specifies bootstrap threshold. | 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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- Y. Yu, T. Warnow, and L. Nakhleh. Algorithms for mdcMDC-based multi-locus phylogeny inference. The 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 531–545531--545, 2011. LNBI 6577.
See Also
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