3.3 Reading trees

input.tree.file = {path}

The phylogenetic tree file to use.

input.tree.format = {Newick|Nexus|NHX}

The format of the input tree file.

In case the input tree does not specify node identifiers, some will be generated automatically. Nodes identifiers can be outputed using the following option:

output.tree_ids.file = {{path}|none}

A tree file in newick format, with node ids instead of bootstrap values, and leaf names with their id as suffix.

In case it is supported by the program, the use of that option will cause the program to exit just after producing the tagged tree.

Some programs may require that your file contains several trees. The corresponding options are then:

input.trees.file = {path}

The file containing multiple trees.

input.trees.format = {Newick|Nexus|NHX}

The format of the input tree file.