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.

                                                    Feb 2018                                        tree-tool(1)