abstract-network(46) approximation(8) APX-hard(2) ARG(5) block-realization(1) bootstrap(3) bound(3) branch-and-bound(1) cactus-graph(1) characterization(6) circular-split-system(6) clustering(2) coalescent(8) consensus(8) consistency(2) cophylogeny(1) distance-between-networks(22) diversity(1) duplication(11) enumeration(4) evaluation(25) explicit-network(89) exponential-algorithm(2) FPT(13) from-clusters(10) from-distances(20) from-multilabeled-tree(6) from-network(10) from-quartets(7) from-rooted-trees(61) from-sequences(37) from-species-tree(26) from-splits(10) from-trees(6) from-triplets(17) from-unrooted-trees(11) galled-network(4) galled-tree(35) generation(8) haplotype-network(2) haplotyping(1) heuristic(9) HMM(2) hybridization(33) inapproximability(5) integer-linear-programming(1) labeling(3) lateral-gene-transfer(34) level-k-phylogenetic-network(19) likelihood(10) lineage-sorting(4) MASN(4) median-network(15) MedianJoining(2) minimum-number(14) minimum-spanning-network(2) model-selection(2) mu-distance(2) NeighborNet(11) nested-network(2) netting(3) normal-network(2) NP-complete(27) optimal-realization(2) parsimony(32) perfect(5) phylogenetic-network(221) phylogeny(218) polynomial(47) Program-Arlequin(5) Program-Beagle(3) Program-Bio-PhyloNetwork(4) Program-CombineTrees(2) Program-constNJ(1) Program-Dendroscope(8) Program-EEEP(3) Program-GalledTree(1) Program-HapBound(1) Program-HorizStory(2) Program-HybridInterleave(2) Program-HybridNumber(3) Program-LatTrans(5) Program-LEV1ATHAN(1) Program-Lev1Generator(1) Program-Level2(2) Program-Marlon(3) Program-McKiTscH(1) Program-MPR(1) Program-MY-CLOSURE(1) Program-Nepal(7) Program-NetGen(3) Program-NetTest(1) Program-NetView(1) Program-Network(5) Program-PADRE(5) Program-Phangorn(1) Program-PhyloNet(8) Program-PIRN(1) Program-Prunier(1) Program-Pyramids(3) Program-QNet(3) Program-Quartet(1) Program-RecMin(1) Program-Recodon(3) Program-RecPars(1) Program-Reticlad(2) Program-Serial-NetEvolve(1) Program-SHRUB(3) Program-Simplistic(3) Program-Sliding-MinPD(1) Program-Spectronet(4) Program-SplitsTree(28) Program-SPNet(5) Program-SPRDist(1) Program-T-REX(10) Program-TCS(8) Program-Treevolve(2) Program-WeakHierarchies(2) pyramid(6) quasi-median-network(2) realization(4) recombination(29) recombination-detection(4) reconstruction(125) regular-network(6) reticulogram(9) serial-evolutionary-networks(1) simulated-annealing(1) simulation(2) site-consistency(1) software(42) split(16) split-decomposition(12) split-network(26) SPR-distance(7) statistical-model(15) statistical-parsimony(4) supernetwork(5) survey(19) time-consistent-network(9) tree-child-network(13) tree-sibling-network(8) tripartition-distance(10) triplet-distance(1) unicyclic-network(2) visualization(21) weak-hierarchy(6) weakly-compatible(3)