Metadata-Version: 2.1
Name: pylabeledrf
Version: 0.2.1
Summary: A package to compute the Robinson Fould distance extended to labeled topologies.
Home-page: https://github.com/dessimozlab/pylabeledrf
Author: Christophe Dessimoz
Author-email: christophe.dessimoz@unil.ch
License: UNKNOWN
Description: # pylabeledrf
        
        pylabeledrf is a heuristic to compute an extension of the Robinson Foulds tree topological distance between labeled topologies, where inner nodes are labeled with speciation or duplication events.
        
        ## Citation
        If you use our package in your work, please consider citing:
        
        Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Manuel Lafond, Gabriela Lobinska, *Extending the Robinson-Foulds distance to reconciled trees*, submitted
        
        
        ## Installation
        
        The package requires Python 3 (>=3.6). The easiest way to install is using 
        `pip`, to install the <a href="https://pypi.org/project/pylabeledrf/">package from 
        PyPI</a>.
        
        ```
        pip install pylabeledrf
        ```
        
        ## Documentation
        
        Documentation is available <a href="http://dessimozlab.github.io/pylabeledrf/build/html/">here</a>.
        
        ## Example
        
        ```python
        from pylabeledrf.computeLRF import *
        import dendropy
        taxa = dendropy.TaxonNamespace()
        
        # retrieve the test TP53 reconciled tree (from Ensembl compara 96)
        p53 = dendropy.Tree.get_from_url(
            'https://raw.githubusercontent.com/DessimozLab/pylabeledrf/master/test/p53.nhx', 
            'newick', taxon_namespace=taxa)
        t1 = parseEnsemblLabels(p53)
        
        # introduce 5 random edits and compute the distance
        t2 = mutateLabeledTree(t1, 5)
        computeLRF(t1,t2)
        
        # randomise the labels and compute the distance
        t3 = randomLabels(t1)
        computeLRF(t1,t3)
        ```
        
        
        ## License
        
        Copyright 2019 Christophe Dessimoz
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
