treeparser.py

Modifies Newick format trees from PAUP (NEXUS format) and phylip phylogenetics 
programs. Can be used to change taxon names, node labels, and branch lengths. The
default input format is from PAUP 4.0b10.

-out           name of outfile. Prints to stdout by default.
-intree        input tree
-fmt           { [nex] | none } tree format
    nex            nexus format
    none           file contains nothing but the parenthesized expression
                   for the tree: "( ... );"
-brlen         add branch labels to intree from this tree in nexus
               format
-nodelab       add node labels to intree. -nodelab with no argument
               assigns (fairly arbitrary) integer values to internal
               nodes. -nodelab=treefile adds node labels (eg bootstrap
               values) specified in a Newick format tree contained
               in treefile. Labels are transferred only if a node
               has an identical set of terminal taxa in both intree
               and the tree specified by -nodelab.
-rmbrlen       remove branch lengths from intree
-rmnode        remove node labels from intree
-namerpl       file directing replacement of names in tree. Format
               is [old name] [new name] Sequence names not found
               in the tree are ignored. 
-h             Prints documentation.
-v             { [1] } verbosity
-version       print version info and exit

$Id: treeparser.py,v 1.1 2004/10/10 02:53:10 nghoffma Exp $