neighbor-net

{{Technical|date=December 2019}}

File:Heterobranchia tree.png generated by SplitsTree v4.6.]]

NeighborNet{{cite journal | vauthors = Bryant D, Moulton V | title = Neighbor-net: an agglomerative method for the construction of phylogenetic networks | journal = Molecular Biology and Evolution | volume = 21 | issue = 2 | pages = 255–65 | date = February 2004 | pmid = 14660700 | doi = 10.1093/molbev/msh018 | doi-access = free }} 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.{{cite journal | vauthors = Bryant D, Moulton V, Spillner A | title = Consistency of the neighbor-net algorithm | journal = Algorithms for Molecular Biology | volume = 2 | pages = 8 | date = June 2007 | pmid = 17597551 | pmc = 1948893 | doi = 10.1186/1748-7188-2-8 | doi-access = free }}{{cite journal | vauthors = Levy D, Pachter L | title = The neighbor-net algorithm. | journal = Advances in Applied Mathematics | date = August 2011 | volume = 47 | issue = 2 | pages = 240–58 | doi = 10.1016/j.aam.2010.09.002 | doi-access = free }} The method is implemented in the SplitsTree and R/Phangorn{{cite journal | vauthors = Schliep KP | title = phangorn: phylogenetic analysis in R | journal = Bioinformatics | volume = 27 | issue = 4 | pages = 592–3 | date = February 2011 | pmid = 21169378 | pmc = 3035803 | doi = 10.1093/bioinformatics/btq706 }}{{cite journal| vauthors = Schliep K, Potts AA, Morrison DA, Grimm GW |date=2017|title=Intertwining phylogenetic trees and networks|journal=Methods in Ecology and Evolution|language=en|volume=8|issue=10|pages=1212–1220|doi=10.1111/2041-210X.12760 |doi-access=free|bibcode=2017MEcEv...8.1212S }} packages.

Examples of the application of Neighbor-net can be found in virology,{{cite journal | vauthors = Schmidt-Chanasit J, Bialonski A, Heinemann P, Ulrich RG, Günther S, Rabenau HF, Doerr HW | title = 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 = Journal of Clinical Virology | volume = 44 | issue = 3 | pages = 235–7 | date = March 2009 | pmid = 19186100 | doi = 10.1016/j.jcv.2008.12.016 }} horticulture,{{cite journal | vauthors = Kilian B, Ozkan H, Deusch O, Effgen S, Brandolini A, Kohl J, Martin W, Salamini F | display-authors = 6 | title = Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes | journal = Molecular Biology and Evolution | volume = 24 | issue = 1 | pages = 217–27 | date = January 2007 | pmid = 17053048 | doi = 10.1093/molbev/msl151 | doi-access = free | hdl = 11858/00-001M-0000-0012-38C8-E | hdl-access = free }} dinosaur genetics,{{cite journal | vauthors = Buckley M, Walker A, Ho SY, Yang Y, Smith C, Ashton P, Oates JT, Cappellini E, Koon H, Penkman K, Elsworth B, Ashford D, Solazzo C, Andrews P, Strahler J, Shapiro B, Ostrom P, Gandhi H, Miller W, Raney B, Zylber MI, Gilbert MT, Prigodich RV, Ryan M, Rijsdijk KF, Janoo A, Collins MJ | display-authors = 6 | title = Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry" | journal = Science | volume = 319 | issue = 5859 | pages = 33; author reply 33 | date = January 2008 | pmid = 18174420 | pmc = 2694913 | doi = 10.1126/science.1147046 | bibcode = 2008Sci...319...33B }} comparative linguistics,{{cite journal|last1=Bowern|first1=Claire|author-link1=Claire Bowern|title=Historical linguistics in Australia: trees, networks and their implications|journal=Philosophical Transactions of the Royal Society B: Biological Sciences|volume=365|issue=1559|year=2010|pages=3845–3854|issn=0962-8436|doi=10.1098/rstb.2010.0013|pmid=21041209|pmc=2981908}} and archaeology.{{cite book | vauthors = Shennan S | title = Pattern and process in cultural evolution. | publisher = University of California Press | date = 2009 }}