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.

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

AUTHORS

Benjamin Redelings.