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"author": "Christophe Dessimoz",
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"description": "# pylabeledrf\n\npylabeledrf 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.\n\n## Citation\nIf you use our package in your work, please consider citing:\n\nSamuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Manuel Lafond, Gabriela Lobinska, *Extending the Robinson-Foulds distance to reconciled trees*, submitted\n\n\n## Installation\n\nThe package requires Python 3 (>=3.6). The easiest way to install is using \n`pip`, to install the package from \nPyPI.\n\n```\npip install pylabeledrf\n```\n\n## Documentation\n\nDocumentation is available here.\n\n## Example\n\n```python\nfrom pylabeledrf.computeLRF import *\nimport dendropy\ntaxa = dendropy.TaxonNamespace()\n\n# retrieve the test TP53 reconciled tree (from Ensembl compara 96)\np53 = dendropy.Tree.get_from_url(\n 'https://raw.githubusercontent.com/DessimozLab/pylabeledrf/master/test/p53.nhx', \n 'newick', taxon_namespace=taxa)\nt1 = parseEnsemblLabels(p53)\n\n# introduce 5 random edits and compute the distance\nt2 = mutateLabeledTree(t1, 5)\ncomputeLRF(t1,t2)\n\n# randomise the labels and compute the distance\nt3 = randomLabels(t1)\ncomputeLRF(t1,t3)\n```\n\n\n## License\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER \nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n\n\n",
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