Many commands use a list of gene trees, which are contained in TREE block, as input. There are two formats.
(gene_tree_ident1 [, gene_tree_ident2...]) |
This format is valid for all commands that require a list of gene trees as input.
({gene_tree_ident1, [, gene_tree_ident2...]} [,{gene_tree_ident3, [, gene_tree_ident4...]}]) |
It is usually used when gene trees are reconstructed from Bayesian method. For example,
#NEXUS
BEGIN TREES;
Tree gt1 = [&W 0.9] ((C,((B,D),A)),E);
Tree gt2 = [&W 0.1] (B,(D,(C,(A,E))));
Tree gt3 = [&W 0.6] (D,(B,((C,E),A)));
Tree gt4 = [&W 0.4] (D,((B,E),(C,A)));
END;
BEGIN PHYLONET;
InferNetwork_ML ({gt1,gt2},{gt3,gt4}) 1;
END; |
where gt1 and gt2 (and gt3 and gt4) are trees from one locus with posterior probabilities.
Or bootstrapping.
#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_ML ({gt1-gt100},{gt101-gt200}) 1;
END; |
where gt1 to gt100 (and gt101 to gt200) are 100 bootstrap replicates from one locus.
Note that this format is only valid for command InferNetwork_ML and CalGTProb.
using '-' : trees are named continuously with the same prefix
#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; |
#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; |