Formats

Many commands use a list of gene trees, which are contained in TREE block, as input. There are two formats.

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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
  html lang
  #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
  html lang
  #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;