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Philippe Gambette,
Leo van Iersel,
Mark Jones,
Manuel Lafond,
Fabio Pardi and
Celine Scornavacca. Rearrangement Moves on Rooted Phylogenetic Networks. In PLoS Computational Biology, Vol. 13(8):e1005611.1-21, 2017. Keywords: distance between networks, explicit network, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance. Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/.
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Philippe Gambette,
Leo van Iersel,
Steven Kelk,
Fabio Pardi and
Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):1773-1795, 2016. Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network. Note: http://arxiv.org/abs/1607.06285.
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Bui Quang Minh,
Fabio Pardi,
Steffen Klaere and
Arndt von Haeseler. Budgeted Phylogenetic Diversity on Circular Split Systems. In TCBB, Vol. 6(1):22-29, 2009. Keywords: abstract network, circular split system, dynamic programming, from network, phylogenetic network, polynomial, split, split network. Note: http://dx.doi.org/10.1109/TCBB.2008.54.
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"In the last 15 years, Phylogenetic Diversity (PD) has gained interest in the community of conservation biologists as a surrogate measure for assessing biodiversity. We have recently proposed two approaches to select taxa for maximizing PD, namely PD with budget constraints and PD on split systems. In this paper, we will unify these two strategies and present a dynamic programming algorithm to solve the unified framework of selecting taxa with maximal PD under budget constraints on circular split systems. An improved algorithm will also be given if the underlying split system is a tree. © 2006 IEEE."
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Hadas Birin,
Zohar Gal-Or,
Isaac Elias and
Tamir Tuller. Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. In WABI07, Vol. 4645:111-123 of LNCS, springer, 2007. Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction. Note: http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf.
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Katharina Huber,
Michael Langton,
David Penny,
Vincent Moulton and
Mike Hendy. Spectronet: A package for computing spectra and median networks. In ABIO, Vol. 1(3):159-161, 2004. Keywords: from splits, median network, phylogenetic network, phylogeny, Program Spectronet, software, split, visualization. Note: http://citeseer.ist.psu.edu/631776.html.
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Spectronet is a package that uses various methods for exploring and visualising complex evolutionary signals. Given an alignment in NEXUS format, the package works by computing a collection of weighted splits or bipartitions of the taxa and then allows the user to interactively analyse the resulting collection using tools such as Lento-plots and median networks. The package is highly interactive and available for PCs.
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