Formats
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.
(gene_tree_ident1 [, gene_tree_ident2...])
This format is valid for all commands that require a list of gene trees as input.
- One is delimited list of sets of gene tree identifiers, as below, where gene trees in the same set are from one locus.
({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.
Abbreviation
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;
- using 'all' : all trees in TREES block will be used
#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;