NAME

tree-reroot - Place the root at a selected node or branch.

SYNOPSIS

tree-reroot TREE --outgroup NAME

tree-reroot TREE --taxa LIST

tree-reroot TREE --leaf NAME

tree-reroot TREE --parent-of NAME

tree-reroot TREE --branch SPLIT

DESCRIPTION

Change the root of the first tree in a file and write one Newick tree to standard output. Choose an existing node with --taxa, --leaf, or --parent-of, or insert a root halfway along a branch with --outgroup or --branch.

Rerooting changes the orientation used to write the tree. It does not prune leaves or automatically suppress the former root if that node has degree two. Splitting a branch replaces its length with two equal halves, preserving leaf-to-leaf distances. The branch-splitting modes require branch lengths.

At least one selector is required. If several are supplied, the first present in this list wins: --outgroup, --taxa, --leaf, --parent-of, --branch. The other selectors are ignored.

INPUT

TREE is a positional Newick or NEXUS filename; only its first tree is used. - is not a standard-input alias. Names must match the tree's taxon labels.

OPTIONS

-h, --help

Print help and exit.

--outgroup NAME

Insert the root halfway along the branch leading to this leaf. The outgroup is supplied with this option, not as a second positional argument.

--taxa LIST

Root at the node where the paths connecting three specified taxa meet. Supply exactly three names, separated by commas, or use @filename to read names separated by commas or newlines. Empty entries are ignored. Prefix an initial literal @ with a backslash to avoid reading a file.

--leaf NAME

Use this leaf node itself as the root. This differs from inserting a root along its branch and can produce a Newick tree with a named degree-one root.

--parent-of NAME

Root at the node adjacent to this leaf. The selected node does not depend on the current orientation of the tree.

--branch SPLIT

Insert the root halfway along the branch matching a partition. Supply a quoted, space-separated expression such as 'A B | C D', with | as a separate token. The expression may specify a partial partition, but it must identify a matching branch. This syntax cannot represent names containing spaces. The requested and matched partitions are also printed to standard error.

EXAMPLES

For a file tree.nwk containing ((A:1,B:1):2,C:1,D:1);:

tree-reroot tree.nwk --outgroup D > rooted.nwk
tree-reroot tree.nwk --taxa A,C,D
tree-reroot tree.nwk --parent-of A
tree-reroot tree.nwk --leaf D
tree-reroot tree.nwk --branch 'A B | C D'

SEE ALSO

tree-tool(1), tree-partitions(1)

REPORTING BUGS

BAli-Phy online help: https://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.