Man page - tree-tool(1)

Packages contains this manual

Package:  bali-phy
apt-get install bali-phy

Manuals in package:
• alignment-consensus(1)
• cut-range(1)
• alignment-thin(1)
• alignment-max(1)
• bali-phy-pkg(1)
• bp-analyze(1)
• alignment-draw(1)
• summarize-ancestors(1)
• extract-ancestors(1)
• stats-select(1)
• mctree-mean-lengths(1)
• trees-consensus(1)
• alignment-find(1)
• bali-phy(1)
• statreport(1)
• alignment-indices(1)
• tree-mean-lengths(1)
• pickout(1)
• draw-tree(1)
• alignment-gild(1)
• alignment-distances(1)
• alignment-info(1)
• tree-tool(1)
• alignments-diff(1)
• trees-bootstrap(1)
• mcon-tool(1)
• alignment-cat(1)
• alignment-chop-internal(1)
• alignment-translate(1)
• trees-distances(1)
• bali-subsample(1)
Documentations in package:
• bali-phy

Manual

tree-tool

NAME
SYNOPSIS
DESCRIPTION
GENERAL OPTIONS:
MODIFICATION OPTIONS:
OUTPUT OPTIONS:
REPORTING BUGS:
AUTHORS

---

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.

---