utcs Phylogenetics
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checkIfPlenary.py

  • % ./checkIfPlenary.py -h
                      
    Usage: checkIfPlenary.py [options]
    
    This script reads a set of source trees and a set of supertrees on those
    source trees as inputs.  If any of the supertrees are non-plenary, a summary
    message is printed along with a list containing only the plenary supertrees.
    All trees must be specified in Newick format.
    
    Options:
      -h, --help            show this help message and exit
      -t FILE, --trees=FILE
                            read estimate trees from FILE
      -s FILE, --sources=FILE
                            read source trees from FILE
                      

getFpFn.py

  • % ./getFpFn.py -h
    Usage: getFpFn.py [options]
    
    This script prints the FP rate, FN rate, and Robinson-Foulds distance between
    a pair of trees.  Each tree must be specified in Newick format.
    
    Options:
      -h, --help            show this help message and exit
      -t FILE, --true=FILE  read true tree from FILE
      -e FILE, --estimate=FILE
                            read estimate tree from FILE
                      

getGreedyConsensus.py

  • % ./getGreedyConsensus.py -h
    Usage: getGreedyConsensus.py [options]
    
    This script prints the greedy consensus of a set of trees, as calculated by
    PAUP*.  Trees must be specified in Newick format.
    
    Options:
      -h, --help            show this help message and exit
      -t FILE, --trees=FILE
                            read supertrees from FILE
      -s FILE, --sources=FILE
                            read source trees from FILE
                      

getNumSharedBipartitions.py

  • % ./getNumSharedBipartitions.py -h
    Usage: getNumSharedBipartitions.py tree1 tree2
    
    This script prints the number of bipartitions common to both input trees.
    Trees must be specified in Newick format.
    
    Options:
      -h, --help  show this help message and exit
                      

getResolution.py

  • % ./getResolution.py -h
    Usage: getResolution.py [options] < input > output
    
    This script reads a tree and prints its resolution, defined as the number of
    internal edges in the tree divided by n - 3, where n denotes the number of
    leaves in the tree.  The tree must be specified in Newick format.
    
    Options:
      -h, --help           show this help message and exit
      -i FILE, --in=FILE   read tree from FILE
      -o FILE, --out=FILE  write output to FILE
                      

getSumOfFpFnRf.py

  • % ./getSumOfFpFnRf.py -h
    Usage: getSumOfFpFnRf.py [options]
    
    This script reads a tree and a set of source trees and prints the SumFP,
    SumFN, and SumRF scores of the tree. All trees must be specified in Newick
    format.
    
    Options:
      -h, --help            show this help message and exit
      -t FILE, --tree=FILE  read estimate tree from FILE
      -s FILE, --sources=FILE
                            read source trees from FILE
                      

makeRatchetFile.py

  • % ./makeRatchetFile.py -h
    Usage: makeRatchetFile.py [options] < input > output
    
    This script writes a Nexus file with a matrix of binary character encodings of
    the trees read from input followed by PAUP* commands for performing a
    ratcheted MRP analysis.  Trees must be specified in Newick format.
    
    Options:
      -h, --help            show this help message and exit
      -i FILE, --input=FILE
                            read Newick input from FILE
      -o FILE, --output=FILE
                            write Nexus output to FILE
      -p STRING, --prefix=STRING
                            use STRING as prefix for PAUP* output files, [default:
                            'ratchet']
                      

printPolytomyInfo.py

  • % ./printPolytomyInfo.py -h
    Usage: printPolytomyInfo.py [options] < input > output
    
    This script reads an input tree and prints the degrees of polytomies and the
    number of such occurrences in the tree. The tree must be specified in Newick
    format.
    
    Options:
      -h, --help           show this help message and exit
      -i FILE, --in=FILE   read tree from FILE
      -o FILE, --out=FILE  write output to FILE
                      
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