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ms609
TreeDist:Calculate and Map Distances Between Phylogenetic Trees
Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits.
Maintained by Martin R. Smith. Last updated 1 months ago.
phylogeneticstree-distancephylogenetic-treestree-distancestreescpp
137.9 match 32 stars 10.32 score 97 scripts 5 dependentsms609
TBRDist:Rearrangement Distances Between Unrooted Phylogenetic Trees
Fast calculation of the Subtree Prune and Regraft (SPR), Tree Bisection and Reconnection (TBR) and Replug distances between unrooted trees, using the algorithms of Whidden and Matsen (2017) <arxiv:1511.07529>.
Maintained by Martin R. Smith. Last updated 4 years ago.
phylogeneticstree-distancedistance-calculationphylogenetic-treescpp
45.1 match 3.70 score