svr_reroot_tree

Reroot a tree at a different node or a point on an internal arc.

Introduction

Examples:

    svr_reroot_tree -m < tree.nwk > rerooted.tree.wk [to midpoint of tree (an approximation of that)]
    svr_reroot_tree 'Deh.eth.19,Sph.the.DS,Deh.sp.CBD' < tree.nwk > rerooted.tree.nwk [at a node in an unrooted tree]
    svr_reroot_tree 'Deh.eth.19,Deh.sp.CBD' < tree.nwk > rerooted.tree.nwk [at an internal node in a rooted tree]
    svr_reroot_tree 'Deh.eth.19'            < tree.nwk > rerooted.tree.nwk [at a tip]
    svr_reroot_tree -t 'Deh.eth.19'            < tree.nwk > rerooted.tree.nwk [at a node next to a tip]

To reroot to a point on an arc between two nodes, use

       svr_reroot_tree -f 0.5 NODE1 NODE2 < tree.nwk > rerooted.tree.nwk [NODE1 and NODE2 can be 1, 2,or 3 ids]
e.g.,  
       svr_reroot_tree -f 0.5 Deh.eth.19 'Deh.eth.19,Deh.sp.CBD' < tree.nwk > rerooted.tree.nwk [NODE1 and NODE2 can be 1, 2,or 3 ids]
or     svr_reroot_tree -d 1.5 Deh.eth.19 'Deh.eth.19,Deh.sp.CBD' < tree.nwk > rerooted.tree.nwk [NODE1 and NODE2 can be 1, 2,or 3 ids]

Command-Line Arguments

The program is invoked using

    svr_reroot_tree [-m] [-t] [-f Fraction] [-d Distance] Node(s)

    The operation may require one or two nodes to be specified; these
    immediately follow the optional arguments.  A node is specified
    as a string containing 1 to 3 IDs comma-separated.

-m

Root at the midpoint of the tree (an approximation)

-t

Root at the parent node of the specified tip (i.e., there should be a single node given, and it should be a single tip ID).

-f=Fraction

Specifies the fraction along the path from NODE1 to NODE2 that you wish to place the root at

-d=Distance

Specifies the distance along the path from NODE1 to NODE2 that you wish to place the root at

Output

A rerooted tree in newick format.