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).
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
The package requires Python 3 (>=3.6). The easiest way to install is using
pip, to install the package from
pip install pylabeledrf
Documentation is available here.
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)
Copyright 2019-2020 Christophe Dessimoz
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