---
name: "tree-tool"
section: "1"
platform: "linux"
package: "bali-phy"
version: "4.0-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/tree-tool"
---

# tree-tool(1)

Perform various operations on Newick trees.

## NAME

**tree-tool** - Perform various operations on Newick trees.

## SYNOPSIS

**tree-tool** *tree-file* \[OPTIONS\]

## DESCRIPTION

Perform various operations on Newick trees.

## GENERAL OPTIONS:

- **-h**, **–help**

  produce help message

- **-V**, **–verbose**

  Output more log messages on stderr.

## MODIFICATION OPTIONS:

- **–prune** *arg*

  Comma-separated taxa to remove

- **–root**

  Find a root position

- **–resolve**

  Resolve polytomies

- **–remove-root-branch**

  Remove single branch from root.

- **–remove-root-branches**

  Ensure root is not a tip.

- **–remove-knuckles**

  Remove degree-2 nodes.

- **–scale** *arg*

  Scale branch-lengths by factor

- **–strip-internal-names**

  Remove internal node names

- **–name-all-nodes**

  Add node names

## OUTPUT OPTIONS:

- **–length**

  Report the total tree length

- **–diameter**

  Report the tree diameter

- **–count-leaves**

  Show the number of leaves

- **–count-nodes**

  Show the number of nodes

- **–show-leaves**

  Show the leaf names

- **–show-nodes**

  Show the node names

## REPORTING BUGS:

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\\c .

Please send bug reports to ⟨bali-phy-users@googlegroups.com⟩\\c .

## AUTHORS

Benjamin Redelings.