NAME

tree-partitions - Print branch partitions or information about one tree.

SYNOPSIS

tree-partitions TREE OPTIONS

DESCRIPTION

Print the splits of the leaf set induced by the internal branches of a tree. Cutting a branch divides the leaves into two groups; these groups describe its partition. With --all, include leaf branches, which separate one leaf from all the others.

Alternatively, --info prints structural information, and --scale writes a tree with scaled branch lengths. These modes are selected in that order: --info takes precedence over --scale, which takes precedence over partition output. --all affects only partition output.

INPUT

TREE is a positional Newick or NEXUS filename. Only its first tree is used. This command requires a file; - is not a standard-input alias.

OUTPUT

Partitions are written to standard output, with spaces between leaf names, a | between the two groups, and a blank line between partitions. For example, A B | C D separates A and B from C and D. The two sides describe an unordered split: swapping them does not change the partition.

Output is per branch, not per distinct split. Degree-two nodes can therefore produce repeated splits, and an internal branch can separate a single leaf when a degree-two node lies along its path. The command does not suppress these nodes or combine repeated partitions.

Information output includes node and branch counts, the label count, counts of degree-two and degree-four-or-higher nodes, and whether the tree is a simple bifurcating or multifurcating tree. These are undirected node degrees; an artificial degree-two Newick root contributes to the degree-two count.

Scaling output is one Newick tree. Leaf ordering is standardized before output; the command does not preserve the input's Newick layout or designated root as a rooted representation.

OPTIONS

-h, --help

Print help and exit.

--all

Include partitions from leaf branches as well as internal branches.

--info

Print structural information instead of partitions.

--scale FACTOR

Multiply each branch length by FACTOR and print the resulting tree. Supply a tree with branch lengths for this mode.

EXAMPLES

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

tree-partitions tree.nwk
tree-partitions tree.nwk --all
tree-partitions tree.nwk --info
tree-partitions tree.nwk --scale 0.5 > scaled.nwk

SEE ALSO

tree-tool(1), tree-reroot(1), trees-consensus(1)

REPORTING BUGS

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

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