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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] |
gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited set list of gene tree identifiers. See details. | mandatory |
-e proportion | Get optimal and sub-optimal trees. | optional |
-x | Use all clusters in generation. | optional |
-b threshold | Specifies 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 |
-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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#NEXUS BEGIN TREES; Tree g1 = ((((a1::.550,b1::.550)::.550,c::.550)::.550,d::.550)::.550,e::.550)::.550; Tree g2 = ((a2::.550,b2::.550)::.550,((c::.550,e::.550)::.550,d::.550)::.550)::.550; Tree g3 = ((a::.550,c::.550)::.550,((b::.550,e::.550)::.550,d::.550)::.550)::.550; END; BEGIN PHYLONET; Infer_ST_MDC (g1, g2, g3) -b .5 -e .2 -x -ur -t 1 -a <z:a1,a2,a; y:b1,b2,b; c:c; d:d; e:e>; END; |
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