- Phylogenetic network
A phylogenetic network is "any" graph used to visualize evolutionary relationships between species or organisms. It is employed when reticulate events such as hybridization,
horizontal gene transfer, recombination, or gene duplicationand loss are believed to be involved. Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree.
Many kinds and subclasses of phylogenetic networks have been defined based on the biological phenomenon they represent or which data they are built from (hybridization networks, usually built from rooted trees, recombination networks from binary sequences, median networks from a set of splits, optimal realizations and reticulograms from a
distance matrix), or restrictions to get computationally tractable problems (galled trees, and their generalizations level-k phylogenetic networks, tree-child or tree-sibling phylogenetic networks).
D. H. Huson and D. Bryant, [http://dx.doi.org/10.1093/molbev/msj030 Application of Phylogenetic Networks in Evolutionary Studies] , "Mol. Biol. Evol.", 23(2):254-267, 2006.
Makarenkov, V., Kevorkov, D. and Legendre, P. (2006), [http://biol10.biol.umontreal.ca/makarenv/MKL_article.pdf Phylogenetic Network Reconstruction Approaches] , Applied Mycology and Biotechnology, International Elsevier Series, vol. 6. Bioinformatics, 61-97.
oftware to compute phylogenetic networks
* [http://www.fluxus-engineering.com/sharenet.htm Network] , Free Phylogenetic Network Software. Network generates evolutionary trees and networks from genetic, linguistic, and other data.
* [http://evolution.genetics.washington.edu/phylip/software.html Phylogeny programs] , some of which compute phylogenetic networks
* [http://www.lirmm.fr/~gambette/PhylogeneticNetworks/show.php?keyword=programs List of programs for phylogenetic network reconstruction, evaluation, visualization, etc.]
* [http://www.trex.uqam.ca/index.php?action=hgt&project=trex Network inferring on the T-REX server]
* [http://darwin.uvigo.es TCS] , Phylogenetic networks from DNA sequences or nucleotide distances using statistical parsimony.
*A [http://www-ab.informatik.uni-tuebingen.de/research/phylonets/ismb2005.pdf tutorial] that reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, their definition and interpretation.
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