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.