MC-Net: A method for the construction of phylogenetic networks based on the Monte-Carlo method

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Eslahchi, Changiz ^a   Habibi, Mahnaz ^a   Hassanzadeh, Reza ^a,b   Mottaghi, Ehsan ^a  

^a SHAHID BEHESHTI UNIVERSITY   (Iran)

^b INSTITUTE FOR STUDIES IN THEORETICAL PHYSICS AND MATHEMATICS IPM   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; DATA SET; EVOLUTIONARY THEORY; HEURISTICS; MONTE CARLO ANALYSIS; PHYLOGENETICS;

ALGORITHM; ARTICLE; BIOLOGY; METHODOLOGY; MONTE CARLO METHOD; PHYLOGENY; THEORETICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, THEORETICAL; MONTE CARLO METHOD; PHYLOGENY;

EID: 77955673310     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-254     Document Type: Article

References (20)

1. Phylogenetic analysis: concepts and methods. KK Kidd LA Sgamarella-Zonta, Am J Human Genetics 1971 23 235 252
2. Phylogenetic analysis: models and estimating procedures. LL Cavalli-Sforza AWF Edwards, Am J Hum Genet 1967 19 233 257 (1967) 6026583
3. Construction of phylogenetic trees. WM Fitch E Margoliash, Science 1967 155 279 284 10.1126/science.155.3760.279 5334057
4. The neighbor joining method: a new method for reconstructing phylogenetic trees. N Saitou N Nei, Molecular Biology and Evolution 1987 4 406 425 3447015
5. Phylogenetic similarity trees. S Sattath A Tversky, Psychometrika 1977 42 319 345 10.1007/BF02293654
6. NeighborNet: An agglomerative method for the construction of planar phylogenetic networks. D Bryant V Moulton, Molecular Biology And Evolution 2004 21 255 265 10.1093/molbev/msh018 14660700
7. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. S Grunewald K Forslund A Dress V Moulton, Molecular Biology and Evolution 2007 24 532 538 10.1093/molbev/msl180 17119010
8. Theoretical foundation of the minimum-evolution method of phylogenetic inference. A Rzhetsky M Nei, Mol Biol Evol 1993 10 1073 1095 8412650
9. Neighbor-joining revealed. O Gascuel M Steel, Molecular Biology and Evolution 2006 23 1997 2000 10.1093/molbev/msl072 16877499
10. Split decomposition: A new and useful approach to phylogenetic analysis of distance data. HJ Bandelt AWM Dress, Mol Phyl Evol 1992 1 242 252 10.1016/1055-7903(92)90021-8
11. SplitsTree: A program for analyzing and visualizing evolutionary data. DH Huson, Bioinformatics 1998 14 10 68 73 10.1093/bioinformatics/14.1.68 9520503
12. The Neighbor-Net Algorithm. D Levy L Patcher, Advances in Applied Mathematics 20161590
13. The Minimum-Evolution Distance Based Approach to Phylogenetic Inference. R Desper O Gascuel, Math Evolution and Phylogeny Oxford Univ. Press, Gascuel O, 2005
14. Cyclic permutations and evolutionary trees. C Semple M Steel, Adv Appl Math 2004 32 4 669 680 10.1016/S0196-8858(03)00098-8 (Pubitemid 38670596)
15. C Semple M Steel, Phylogenetics Oxford, UK: Oxford University Press 2003
16. Constructing splits graphs. A Dress DH Huson, IEEE/ACM Transactions in Computational Biology and Bioinformatics 2004 1 109 115 10.1109/TCBB.2004.27 (Pubitemid 40325598)
17. A canonical decomposition theory for metrics on a finite set. H-J Bandelt A Dress, Adv Math 1992 92 47 105 10.1016/0001-8708(92)90061-O
18. A Fast Non-negativity-constrained Least Squares Algorithm. R Bro SD Jong, Journal of Chemometrics 1997 11 5 393 401 10.1002/(SICI)1099-128X(199709/10)11: 5<393::AID-CEM483>3.0.CO;2-L
19. Application of phylogenetic networks in evolutionary studies. D Huson D Bryant, Molecular Biology and Evolution 2005 23 254 267 10.1093/molbev/msj030 16221896
20. P Clote R Backofen, Computational molecular biology New York, WILEY 2000