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.