A fast tool for minimum hybridization networks

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Chen, Zhi Zhong ^a   Wang, Lusheng ^b   Yamanaka, Satoshi ^a  

^a TOKYO DENKI UNIVERSITY   (Japan)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL PROBLEM; EXECUTABLES; EXPERIMENTAL DATUM; FAST ALGORITHMS; FAST TOOL; FOLLOWING PROBLEM; INPUT SIZE; MULTITHREADED; PHYLOGENETIC TREES; PREPROCESS; SEARCH TREES; SIMULATED DATASETS; SINGLE-THREADED; SUB-PROBLEMS; WINDOWS 7; WINDOWS XP;

ALGORITHMS; BIOINFORMATICS; BIOLOGY; COMPUTER OPERATING SYSTEMS; FORESTRY;

PROBLEM SOLVING;

ALGORITHMS; FORESTRY; PROBLEM SOLVING;

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETICS; HYBRIDIZATION; METHODOLOGY; PHYLOGENY; POACEAE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HYBRIDIZATION, GENETIC; PHYLOGENY; POACEAE; SOFTWARE;

EID: 84863093047     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-155     Document Type: Article

References (20)

1. Hein J, Jing T, Wang L, Zhang K. On the complexity of comparing evolutionary trees. Discrete Appl Math 1996, 71:153-169.
2. Bordewich M, Semple C. On the computational complexity of the rooted subtree prune and regraft distance. Ann Combinatorics 2005, 8:409-423.
3. Bordewich M, Semple C. Computing the minimum number of hybridization events for a consistent evolutionary history. Discrete Appl Mathematics 2007, 155:914-928.
4. Albrecht B, Scornavacca C, Cenci A, Huson D. Fast computation of minimum hybridization networks. Bioinformatics 2011, 28:191-197.
5. Collins L, Linz S, Semple C. Quantifying hybridization in realistic time. J Comput Biol 2011, 18:1305-1318. 10.1089/cmb.2009.0166, 21210735.
6. Chen ZZ, Wang L. HybridNet: A tool for constructing hybridization networks. Bioinformatics 2010, 26:2912-2913. 10.1093/bioinformatics/btq548, 20871109.
7. Wu Y. A practical method for exact computation of subtree prune and regraft distance. Bioinformatics 2009, 25:190-196. 10.1093/bioinformatics/btn606, 19019848.
8. Wang J, Wu Y. Fast computation of the exact hybridization number of two phylogenetic trees. Proceedings of the 6th International Symposium on Bioinformatics Research and Applications: 23-26 May 2010; Storrs. 2010, 203-214. M Borodovsky ea .
9. Hill T, Nordström KJ, Thollesson M, Säfström TM, Vernersson AK, Fredriksson R, Schiöth HB. SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees. BMC Evolutionary Biol 2010, 10:42.
10. Cardona G, Rossello F, Valiente G. Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinf 2008, 9:532.
11. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinf 2007, 8:460-460.
12. Beiko R, Hamilton N. Phylogenetic identification of lateral genetic transfer events. BMC Evol Biol 2006, 6:159-169.
13. Group GPW. Phylogeny and subfamilial classification of the grasses (poaceae). Ann Mo Bot Gard 2001, 88:373-457.
14. Schmidt HA. Phylogenetic trees from large datasets. PhD thesis 2003, Heinrich-Heine-Universitat, Dusseldorf.
15. Bordewich M, Semple C. Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable. IEEE/ACM Trans Comput Biol Bioinf 2007, 4:458-466.
16. Whidden C, Beiko RG, Zeh N. Fast FPT algorithms for computing rooted agreement forest: theory and experiments. Proceedings 9th Int Symp Exp Algorithms 20-22 May 2010; Ischia Island 2010, 141-153. Fest P.
17. Wu Y. Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees. Bioinformatics [ISMB] 2010, 26(12):140-148.
18. Baroni M, Grunewald S, Moulton V, Semple C. Bounding the number of hybridisation events for a consistent evolutionary history. J Math Biol 2005, 51:171-182. 10.1007/s00285-005-0315-9, 15868201.
19. Chen ZZ, Wang L. Algorithms for reticulate networks of multiple phylogenetic trees. IEEE/ACM Trans Comput Biol Bioinf 2012, 9:372-384.
20. Baroni M, Semple C, Steel M. Hybrids in real time. Syst Biol 2006, 55:46-56. 10.1080/10635150500431197, 16507523.