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Many commands use a list of gene trees, which are contained in TREE block, as input. There are two formats.
One is comma delimited list of gene tree identifiers, as below, which indicates each tree is from a different locus.
Code Block |
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(gene_tree_ident1 [, gene_tree_ident2...]) |
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Note that this format is only valid for command InferNetwork_ML and CalGTProb.
Abbreviation
using '-' : trees are named continuously with the same prefix
Code Block |
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#NEXUS
BEGIN TREES;
Tree gt1 = ((C,((B,D),A)),E);
Tree gt2 = (B,(D,(C,(A,E))));
......
Tree gt200 = (D,((B,E),(C,A)));
END;
BEGIN PHYLONET;
InferNetwork_MP (gt1-gt200) 1;
END; |
- using 'all' : all trees in TREES block will be used
Code Block |
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#NEXUS
BEGIN TREES;
Tree gt1 = ((C,((B,D),A)),E);
Tree gt2 = (B,(D,(C,(A,E))));
......
Tree gt200 = (D,((B,E),(C,A)));
END;
BEGIN PHYLONET;
InferNetwork_MP (all) 1;
END; |