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Infers the species tree using the “Minimize Deep Coalescence” (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.
The resulting species trees are displayed with the number of extra lineages in each branch. For example, consider the following inferred species tree:
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((a:0,b:0):2,(c:0,d:0):1):0
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In this species tree, there are two extra lineages in branch between node (a, b) and the root, and one extra lineage in branch between node (c, d) and the root. All other branches have 0 extra lineages.
Usage
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infer_ST_MDC {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="4a4891ac6fbffb53-0fec5136-45364683-bcfca2b7-cf6e233d263cb3d0a7e8a738"><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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