addNodeCounts ( origDict )

Add labels at the nodes corresponding to the numbers of the node keys in origDict. Returns a NEW treeDict - does not modify the original

findChildren ( treeDict,  v=1 )

Modifies the named treeDict so that that children field reflects the actual list of names and not the node tags. Also changes all children lists to tuples

main ()

%(filename)s

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 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 verbosity 1}} {{version print version info and exit}}

%(version)s

nodeToDict ( node,  v=1 )

Parses a single node and returns a dict Typical node structure: (3:0.008906,4:0.001323)100

readNexusFile ( instring )

Reads one tree from a nexus format file. A dictionary with the keys treename, tag, and treestring.

reconstructNode ( nodeDict )

Reconstructs a node from a nodeDict having typical structure (3:0.008906,4:0.001323)100 {'taxa': [(3, :0.008906), (4, :0.001323)], 'nodelab': '100'}

reconstructTree ( treeDict )

Reconstructs a dictionary of nodeDict dictionaries (ie, output from treeparse()) into a tree.

removeBranchLenghts ( origDict )

Remove branch lengths from a treedict. Returns a NEW treeDict - does not modify the original

removeNodeLabels ( origDict )

Remove node labels (eg, bootstrap values) from a treedict. Returns a NEW treeDict - does not modify the original

transferNodeLabels (
        toTreeDict,
        fromTreeDict,
        v=0,
        )

Transfer node labels at all nodes having all terminal taxa (children) in common

treeparse ( treestring,  v=1 )

Parse a Newick format tree, break it down into nodes, and return a dictionary.