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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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inferSTinfer_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 NETWORKSTREES; NetworkTree g1 = ((((a,b),c),d),e); NetworkTree g2 = ((a,b),((c,e),d)); NetworkTree g3 = ((a,c),((b,e),d)); END; BEGIN PHYLONET; Infer_ST_MDC (g1, g2, g3); END; |
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#NEXUS BEGIN NETWORKSTREES; NetworkTree g1 = ((((a1::.550,b1::.550)::.550,c::.550)::.550,d::.550)::.550,e::.550)::.550; NetworkTree g2 = ((a2::.550,b2::.550)::.550,((c::.550,e::.550)::.550,d::.550)::.550)::.550; NetworkTree g3 = ((a::.550,c::.550)::.550,((b::.550,e::.550)::.550,d::.550)::.550)::.550; END; BEGIN PHYLONET; InferSTInfer_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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