NAME

       tree_doctor - Scale, prune, merge, and otherwise tweak phylogenetic trees.

DESCRIPTION

       Scale,  prune,  merge,  and  otherwise tweak phylogenetic trees.  Expects input to be a tree model (.mod)
       file unless filename ends with '.nh' or -n option is used, in which case it will be expected to be a tree
       file in Newick format.

USAGE

       tree_doctor [OPTIONS] <file.mod>|<file.nh>

OPTIONS

       --prune, -p <list> Remove all leaves whose names are included in the given list  (comma-separated),  then
              remove  nodes  and  combine  branches  to  restore as a complete binary tree (i.e., with each node
              having zero children or two children).  This option is applied *before* all other options.

       --prune-all-but, -P <list>

              Like --prune, but remove all leaves *except* the ones specified.

       --get-subtree, -g <node_name> Like --prune, but remove all  leaves  who  are  not  descendants  of  node.
              (Note: implies --name-ancestors if given node not explicitly named in input tree)

       --rename,  -r  <mapping>  Rename leaves according to the given mapping.  The format of <mapping> must be:
              "oldname1 -> newname1 ; oldname2 -> newname2 ; ...".  This option is  applied  *after*  all  other
              options (i.e., old names will be used for --prune, --merge, etc.)

       --scale, -s <factor>

              Scale all branches by the specified factor.

       --name-ancestors, -a

       Ensure names are assigned to all ancestral nodes.
              If a node

              is  unnamed,  create  a name by concatenating the names of a leaf from its left subtree and a leaf
              from its right subtree.

       --label-subtree, -L <node[+]:label> Add a label to the subtree of the named node.  If the node name

              is followed by a "+" sign, then the branch leading to that node is included in the subtree.   This
              may  be  used  multiple times to add more than one label, though a single branch may have only one
              label.  --label-subtree and --label-branches options are parsed in the order given, so that  later
              uses may override earlier ones.  Labels are applied *after* all pruning, re-rooting, and re-naming
              options are applied.

       --label-branches, -l <branch1,branch2,...:label>

       Add a label to the branches listed.
              Branches are named by the name

       of the node which descends from that branch.
              See --label-subtree

              above for more information.

       --tree-only, -t Output tree only in Newick format rather than complete tree model.

       --no-branchlen, -N (Implies --tree-only).  Output only topology in Newick format.

       --dissect,  -d  In  place  of ordinary output, print a description of the id, name, parent, children, and
              distance to parent for each node of the tree.  Sometimes useful for debugging.  Can be  used  with
              other options.

       --branchlen, -b

              In  place  of  ordinary  output,  print  the  total branch length of the tree that would have been
              printed.

       --depth, -D <node_name> In place of ordinary output, report distance from named node to root

       --reroot, -R <node_name>

              Reroot tree at internal node with specified name.

       --subtree, -S <node_name> (for use with --scale) Alter only the  branches  in  the  subtree  beneath  the
              specified node.

       --with-branch, -B <node_name>

              (For  use with --reroot or --subtree) include branch above specified node with subtree beneath it.

       --merge, -m <file2.mod> |  <file2.nh>  Merge  with  another  tree  model  or  tree.   The  primary  model
              (<file.mod>)  must have a subset of the species (leaves) in the secondary model (<file2.mod>), and
              the primary tree must be a proper subtree  of  the  secondary  tree  (i.e.,  the  subtree  of  the
              secondary  tree  beneath the LCA of the species in the primary tree must equal the primary tree in
              terms of topology and species names).  If a full tree model is given for the secondary tree,  only
              the  tree  will  be  considered.   The  merged  tree  model will have the rate matrix, equilibrium
              frequencies, and rate distribution of the primary model, but  a  merged  tree  that  includes  all
              species  from both models.  The trees will be merged by first scaling the secondary tree such that
              the subtree corresponding to the primary tree has equal overall length to the primary  tree,  then
              combining  the  primary tree with the non-overlapping portion of the secondary tree.  The names of
              matching species (leaves) must be exactly equal.

       --extrapolate, -e <phylog.nh> | default Extrapolate to a  larger  set  of  species  based  on  the  given
              phylogeny  (Newick-format).   The  primary  tree  must  be  a  subtree  of  the phylogeny given in
              <phylog.nh>, but it need not be a "proper" subtree (see --merge).  A copy will be created  of  the
              larger phylogeny then scaled such that the total branch length of the subtree corresponding to the
              primary  tree  equals  the  total branch length of the primary tree; this new version will then be
              used in place of the primary tree.  If the string "default" is given instead of a filename, then a
              phylogeny for 25 vertebrate species, estimated from sequence data for Target 1 (CFTR) of the  NISC
              Comparative  Sequencing  Program (Thomas et al., Nature 424:788-793, 2003), will be assumed.  This
              option is similar to merge but differs in that the branch length proportions of  the  output  tree
              come  completely  from  the larger tree and the smaller tree doesn't have to be a proper subset of
              the larger tree.

       --newick,-n

              The input file is in Newick format (necessary if file name does not end in .nh)

       --help, -h Print this help message.

tree_doctor 1.4                                     May 2016                                      TREE_DOCTOR(1)