rSPR

rSPR is a software package for calculating rooted subtree-prune-and-regraft distances and rooted agreement forests. Version 1.2.0 includes an implementation of the cluster reduction and edge protection and is significantly faster than the previous versions in many cases. rSPR is available as C++ source code under the GNU GPL v3. This is free software, and you are welcome to redistribute it under certain conditions; See the README for details.


References in zbMATH (referenced in 16 articles , 1 standard article )

Showing results 1 to 16 of 16.
Sorted by year (citations)

  1. Collienne, Lena; Gavryushkin, Alex: Computing nearest neighbour interchange distances between ranked phylogenetic trees (2021)
  2. Hasić, Damir; Tannier, Eric: Gene tree reconciliation including transfers with replacement is NP-hard and FPT (2019)
  3. Shi, Feng; Chen, Jianer; Feng, Qilong; Wang, Jianxin: A parameterized algorithm for the maximum agreement forest problem on multiple rooted multifurcating trees (2018)
  4. van Iersel, Leo; Kelk, Steven; Stamoulis, Georgios; Stougie, Leen; Boes, Olivier: On unrooted and root-uncertain variants of several well-known phylogenetic network problems (2018)
  5. Whidden, Chris; Matsen, Frederick A. IV: Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph (2017)
  6. Chen, Jianer; Shi, Feng; Wang, Jianxin: Approximating maximum agreement forest on multiple binary trees (2016)
  7. Chen, Zhi-Zhong; Machida, Eita; Wang, Lusheng: An improved approximation algorithm for rSPR distance (2016)
  8. Shi, Feng; Feng, Qilong; You, Jie; Wang, Jianxin: Improved approximation algorithm for maximum agreement forest of two rooted binary phylogenetic trees (2016)
  9. Whidden, Chris; Beiko, Robert G.; Zeh, Norbert: Fixed-parameter and approximation algorithms for maximum agreement forests of multifurcating trees (2016)
  10. Chen, Jianer; Fan, Jia-Hao; Sze, Sing-Hoi: Parameterized and approximation algorithms for maximum agreement forest in multifurcating trees (2015)
  11. Chen, Zhi-Zhong; Fan, Ying; Wang, Lusheng: Faster exact computation of rSPR distance (2015)
  12. Kelk, Steven; Scornavacca, Celine: Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable (2014)
  13. Makarenkov, Vladimir; Boc, Alix; Legendre, Pierre: A new algorithm for inferring hybridization events based on the detection of horizontal gene transfers (2014)
  14. Whidden, Chris; Beiko, Robert G.; Zeh, Norbert: Fixed-parameter algorithms for maximum agreement forests (2013)
  15. Whidden, Chris; Beiko, Robert G.; Zeh, Norbert: Fast FPT algorithms for computing rooted agreement forests: Theory and experiments. Extended abstract (2010) ioport
  16. Whidden, Chris; Zeh, Norbert: A unifying view on approximation and FPT of agreement forests. (Extended abstract) (2009) ioport