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A package to compute the Robinson Fould distance extended to labeled topologies.

Project description

pylabeledrf

pylabeledrf is a package to compute an extension of the Robinson Foulds tree topological distance between labeled topologies, where inner nodes are labeled with speciation or duplication events.

From version 0.2 onwards, pylabeledrf includes two functions:

  • computeLRF(), which computes exactly and efficiently the Labeled Robinson Foulds (LRF).
  • computeELRF(), which is a heuristic to compute the edge-based Labeled Robinson Foulds (ELRF).

Citation

If you use our package in your work, please consider citing:

  • For LRF: Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Yannis Nevers, A linear time solution to the Labeled Robinson-Foulds distance problem, submitted
  • For ELRF: Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Manuel Lafond, Gabriela Lobinska, Extending the Robinson-Foulds distance to reconciled trees, APBC 2020 and BMC Genomics, in press

Installation

The package requires Python 3 (>=3.6). The easiest way to install is using pip, to install the package from PyPI.

pip install pylabeledrf

Documentation

Documentation is available here.

Example

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 2019-2020 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.

Project details


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