Who is Who in Phylogenetic Networks

Publications related to 'Program SPRDist' : SPRDist computes the SPR distance between two rooted trees, and will, in a next version, compute the hybridization number of two rooted trees with an Integer Linear Programming method. It can be downloaded at http://www.engr.uconn.edu/~ywu/SPRDist.html   Order by:   Type | Year

Only And Or     related to: --- abstract network agreement forest AIC ancestral trait reconstruction approximation APX hard ARG bayesian BIC block realization bootstrap bound branch and bound branch length cactus graph characterization cherry-picking circular split system cluster containment clustering coalescent compressed network compression consensus consistency cophylogeny counting database display set distance between networks distinct-cluster network distinguishability diversity duplication dynamic programming enumeration evaluation explicit network exponential algorithm flat FPT from binary characters from binets from clusters from continuous characters from distances from gene order from multilabeled tree from multistate characters from network from NGS data from quarnets from quartets from rooted trees from sequences from species tree from splits from subnetworks from trees from tri-LGT-nets from trinets from triplets from unrooted trees FU-stable network galled network galled tree generation genetically stable network haplotype network haplotyping heuristic History bound HMM hybridization identifiability inapproximability incomplete lineage sorting integer linear programming isomorphism k-reticulated kernelization kth-order reduced network labeling lateral gene transfer level k phylogenetic network LGT network likelihood lineage sorting loss LST distance MASN median network MedianJoining minimal lateral network minimum contradiction minimum number minimum spanning network model selection mrca network MSOL mu distance nearly-stable network NeighborNet nested network netting NNI distance NNI moves normal network NP complete number of vertices optimal realization orchard network orientation outerplanar parental hybridization parsimony partly reduced networks pedigree perfect phylogenetic network phylogeny planar polynomial population genetics Program AdmixTools Program ALE Program Angst Program Arlequin Program ARTNET Program Beagle Program BIMLR Program Bio PhyloNetwork Program BMhyd Program Clustistic Program CMPT Program CombineTrees Program ConsensusNetwork Program constNJ Program CycleKiller Program Dendroscope Program ecceTERA Program EEEP Program FastHN Program FastNet Program FlatNJ Program Frin Program Fylogenetica Program GalledTree Program GraphDTL Program HapBound Program HGT_simul Program HiDe Program HorizStory Program Hybrid-coal Program Hybrid-Lambda Program HybridInterleave Program HybridNET Program HybridNumber Program Hybroscale Program icelu-PhyloNetwork Program IcyTree Program IGNet Program ILPEACE Program JML Program JPrIME-DLTRS Program LatTrans Program LEV1ATHAN Program Lev1Generator Program Level2 Program LGTnetwork Program lingpy Program LNetwork Program MaafB Program Marlon Program MC-Net Program McKiTscH Program Mowgli Program MowgliNNI Program MPNet Program MY CLOSURE Program Nepal Program NetGen Program NetTest Program NetView Program Network Program Notung Program PADRE Program Phangorn Program PhippsNetwork Program PhyloDAG Program PhyloNet Program PhyloNet-HMM Program PhyloNetwork Program PhyloNetworks SNaQ Program PhyloSketch Program PIRN Program PopART Program Prunier Program Pyramids Program QNet Program Quartet Program Quartet Decomposition Program QuartetMethods Program QuartetNet Program QuasiDec Program QuickCass Program RANGER-DTL Program RecMin Program Recodon Program RecPars Program Reticlad Program SAGE Program SAQ-Net Program Serial NetEvolve Program SHRUB Program Simplistic Program Sliding MinPD Program SNSA Program Spectronet Program SplitsTree Program SPNet Program SuperQ Program SylvX Program T REX Program TCGenerators Program TCS Program TERA Program TerminusEst Program Treeduce Program TreeFix-DTL Program TreeMix Program Treevolve Program TriLoNet Program TripNet Program ultra-Net Program Ultranet Program WeakHierarchies Program Xscape pseudo-polynomial pyramid quasi-median network quasi-reticulation-visible network realization recombination recombination detection reconstruction reduced networks regular network reticulation-visible network reticulogram rigidly displaying SAT semidirected network serial evolutionary networks simulated annealing simulation site consistency software split split decomposition split network SPR distance spread stable-child network stack-free network statistical model statistical parsimony statistical test supernetwork survey tanglegram TBR distance temporal-hybridization number time consistent network tree containment tree sibling network tree-based network tree-child network tree-child sequence tripartition distance triplet distance unicyclic network uniqueness unrooted tree-based network valid network visualization weak hierarchy weakly compatible weakly displaying

Associated keywords

agreement-forest explicit-network from-rooted-trees hybridization integer-linear-programming minimum-number phylogenetic-network phylogeny Program-HybridNumber Program-SPRDist SPR-distance

2010

1 Yufeng Wu and Jiayin Wang. Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. In ISBRA10, Vol. 6053:203-214 of LNCS, springer, 2010.   Keywords: agreement forest, explicit network, from rooted trees, hybridization, integer linear programming, minimum number, phylogenetic network, phylogeny, Program HybridNumber, Program SPRDist, SPR distance. Note: http://www.engr.uconn.edu/~ywu/Papers/ISBRA10WuWang.pdf.         Toggle abstract "Hybridization is a reticulate evolutionary process. An established problem on hybridization is computing the minimum number of hybridization events, called the hybridization number, needed in the evolutionary history of two phylogenetic trees. This problem is known to be NP-hard. In this paper, we present a new practical method to compute the exact hybridization number. Our approach is based on an integer linear programming formulation. Simulation results on biological and simulated datasets show that our method (as implemented in program SPRDist) is more efficient and robust than an existing method. © 2010 Springer-Verlag Berlin Heidelberg."