Neighbor-net
NeighborNet[1] is an algorithm for constructing phylogenetic networks which is loosely based on the neighbor joining algorithm. Like neighbor joining, the method takes a distance matrix as input, and works by agglomerating clusters. However, the NeighborNet algorithm can lead to collections of clusters which overlap and do not form a hierarchy, and are represented using a type of phylogenetic network called a splits graph. If the distance matrix satisfies the Kalmanson combinatorial conditions then Neighbor-net will return the corresponding circular ordering.[2][3] The method is implemented in the SplitsTree and R/Phangorn[4][5] packages.
Examples of the application of Neighbor-net can be found in virology,[6] horticulture,[7] dinosaur genetics,[8] comparative linguistics, and archaeology.[9]
References
- ^ Bryant D, Moulton V (February 2004). "Neighbor-net: an agglomerative method for the construction of phylogenetic networks". Molecular Biology and Evolution. 21 (2): 255–65. doi:10.1093/molbev/msh018. PMID 14660700.
- ^ Bryant D, Moulton V, Spillner A (June 2007). "Consistency of the neighbor-net algorithm". Algorithms for Molecular Biology : AMB. 2: 8. doi:10.1186/1748-7188-2-8. PMC 1948893. PMID 17597551.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Levy D, Pachter L (August 2011). "The neighbor-net algorithm". Advances in Applied Mathematics. 47 (2): 240–58. doi:10.1016/j.aam.2010.09.002.
- ^ Schliep KP (February 2011). "phangorn: phylogenetic analysis in R". Bioinformatics. 27 (4): 592–3. doi:10.1093/bioinformatics/btq706. PMC 3035803. PMID 21169378.
- ^ Schliep K, Potts AA, Morrison DA, Grimm GW (2017). "Intertwining phylogenetic trees and networks". Methods in Ecology and Evolution. 8 (10): 1212–1220. doi:10.1111/2041-210X.12760.
- ^ Schmidt-Chanasit J, Bialonski A, Heinemann P, Ulrich RG, Günther S, Rabenau HF, Doerr HW (March 2009). "A 10-year molecular survey of herpes simplex virus type 1 in Germany demonstrates a stable and high prevalence of genotypes A and B". Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology. 44 (3): 235–7. doi:10.1016/j.jcv.2008.12.016. PMID 19186100.
- ^ Kilian B, Ozkan H, Deusch O, Effgen S, Brandolini A, Kohl J, Martin W, Salamini F (January 2007). "Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes". Molecular Biology and Evolution. 24 (1): 217–27. doi:10.1093/molbev/msl151. PMID 17053048.
- ^ M. Buckley and 27 others. Comment on``protein sequences from Mastodon and Tyrannosaurus Rex revealed by mass spectrometry". Science, 319(5859):33, 2008.
- ^ Shennan S (200). Pattern and process in cultural evolution. University of California Press.