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.