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## Missing URL (83 references)

ACSP2012: From Networks to Trees

AEUV2006: Site Consistency in Phylogenetic Networks with Recombination

AJSUV2012: Faster computation of the Robinson–Foulds distance between phylogenetic networks

Albrecht2011: Fast Computation of Hybridization Networks

ALRR2014: Tree-Child Cluster Networks

Bandelt1994: Phylogenetic Networks

Bandelt1995: Combination of data in phylogenetic analysis

BandeltDress1992: A canonical decomposition theory for metrics on a finite set

BandeltDress1994: An order theoretic framework for overlapping clustering

BandeltDress1994b: A relational approach to split decomposition

Bertrand1986: Étude de la représentation pyramidale

BertrandDiday1985: A visual representation of the compatibility between an order and a dissimilarity index: the pyramids

BlairAne2019: Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data

BSM2014: Fishing for minimum evolution trees with Neighbor-Nets

CardonaZhang2020: Counting and Enumerating Tree-Child Networks and Their Subclasses

CCYH2018: Reconstructing One-Articulated Networks with Distance Matrices

CHT2018: Compact Encoding for Galled-Trees and its Applications

DondiPirola2014: Beyond Evolutionary Trees

DRDB2011: Models, algorithms and programs for phylogeny reconciliation

FischerPeters2015: A Practical Succinct Data Structure for Tree-Like Graphs

Fitch2001: Reticulation

FKP2015: A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks

FQH2011: Phylogenetic networks: A tool to display character conflict and demographic history

GauthierLapointe2002: A comparison of alternative methods for detecting reticulation events in phylogenetic analysis

Gorecki2006: Detection of horizontal gene transfer

Gorecki2010: H-trees: a model of evolutionary scenario with horizontal gene transfer

Grant1971: Plant Speciation

GSBBM2013: SuperQ: Computing Supernetworks from Quartets

Hendriksen2018: Tree-based unrooted nonbinary phylogenetic networks

HLMW2016: Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations

HSW2005: The coalescent with recombination

Humphries1983: Primary data in hybrid analysis

HusonScornavacca2012: Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

JanssonLingas2014: Computing the rooted triplet distance between galled trees by counting triangles

JJY2020: Combining Networks Using Cherry Picking Sequences

JMS2019: Computing the Rooted Triplet Distance Between Phylogenetic Networks

KannanWheeler2014: Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming

Lekic2015: Trees, agreement forests and treewidth: combinatorial algorithms for constructing phylogenetic networks

Linz2013: Reticulation

LSD2017: Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses

MBL2014: A New Algorithm for Inferring Hybridization Events Based on the Detection of Horizontal Gene Transfers

McBee2012: Generalizing Fourier Calculus on Evolutionary Trees to Splits Networks

MGL2013: Inferring Phylogenetic Networks from Gene Order Data

MKSWG2017: A Resolution of the Static Formulation Question for the Problem of Computing the History Bound

Morgado2015: Propriétés structurelles et relations des classes de réseaux phylogénétiques

Morrison2010b: Phylogenetic networks in systematic biology (and elsewhere)

Morrison2013: Phylogenetic networks are fundamentally different from other kinds of biological networks

Morrison2014: Is the Tree of Life the Best Metaphor, Model, or Heuristic for Phylogenetics?

Morrison2014a: Phylogenetic Networks: A Review of Methods to Display Evolutionary History

Morrison2014b: Rooted Phylogenetic Networks for Exploratory Data Analysis

Morrison2014c: Next generation sequencing and phylogenetic networks

MoultonHuber2005: Phylogenetic Networks

MoultonHuber2009: Split Networks. A tool for exploring complex evolutionary relationships in molecular data

MWZPLGX2012: Quartet decomposition server: a platform for analyzing phylogenetic trees

Nelson1983: Reticulation in Cladograms

NVPCDB2013: Reconciliation and local gene tree rearrangement can be of mutual profit

OTIM2016: TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories

PhippsBereg2012: Optimizing Phylogenetic Networks for Circular Split Systems

PSC2020: Generation of Level-k LGT Networks

Radice2012: A Bayesian Approach to Modelling Reticulation Events with Application to the Ribosomal Protein Gene rps11 of Flowering Plants

RSDB2016: Inferring gene duplications, transfers and losses can be done in a discrete framework

ShengBereg2012: Approximating Metrics with Planar Boundary-Labeled Phylogenetic Networks

SPC2017: Fast algorithm for the reconciliation of gene trees and LGT networks

TPAE2017: Inferring phylogenies from minimal information

Voorkamp2014b: Maximal Acyclic Agreement Forests

Wagner1983: Reticulistics: the recognition of hybrids and their role in cladistics and classification

WangGuo2019: IGNet: Constructing Rooted Phylogenetic Networks Based on Incompatible Graphs

WangGuo2019b: A review of metrics measuring dissimilarity for rooted phylogenetic networks

Wanntorp1983: Reticulated cladograms and the identification of hybrid taxa

Wen2017: Bayesian Inference of Phylogenetic Networks from Sequence Data

Wetzel1995: Zur Visualisierung abstrakter Ahnlichkeitsbeziehungen

WGLLWXC2013: LNETWORK: An Efficient and Effective Method for Constructing Phylogenetic Networks

WGXCLW2013b: BIMLR: A Method for Constructing Rooted Phylogenetic Networks from Rooted Phylogenetic Trees

WTM2014: A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle

Wu2013b: An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees

WYL2016: Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

WYZN2018: Inferring Phylogenetic Networks Using PhyloNet

YBN2013: Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

YGW2013: Quartet-Net: A Quartet Based Method to Reconstruct Phylogenetic Networks

YRN2013: Fast algorithms and heuristics for phylogenomics under ILS and hybridization

Zhang2019: Clusters, Trees, and Phylogenetic Network Classes

Zhang2020: Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks

ZNWZ2011: Network model and efficient method for detecting relative duplications or horizontal gene transfers

## Missing DOI (138 references)

AEUV2006 (InBook): Site Consistency in Phylogenetic Networks with Recombination

Albrecht2011 (MastersThesis): Fast Computation of Hybridization Networks

Albrecht2014 (Misc): Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests

Albrecht2015a (Misc): Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests

Albrecht2015b (Misc): Fast computation of all maximum acyclic agreement forests for two rooted binary phylogenetic trees

Albrecht2016 (PhdThesis): Computing Hybridization Networks Using Agreement Forests

Ane2017 (Misc): From reconstructing to using phylogenetic networks

Bandelt1992 (Misc): Four-point characterization of the dissimilarity functions obtained from indexed closed weak hierarchies

Bandelt1994 (InProceedings): Phylogenetic Networks

Bao2009 (PhdThesis): Phylogenetic network construction and the application

Baroni2004 (PhdThesis): Hybrid phylogenies : a graph-based approach to represent reticulate evolution

Bastide2017 (PhdThesis): Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies

Bastkowski2013 (PhdThesis): From Trees to Networks and Back

BDDM2008 (InBook): The Comparison of Phylogenetic Networks: Algorithms and Complexity

Bertrand1986 (PhdThesis): Étude de la représentation pyramidale

BertrandDiday1985 (Article (Journal)): A visual representation of the compatibility between an order and a dissimilarity index: the pyramids

BertrandDiday1990 (Article (Journal)): Une généralisation des arbres hiérarchiques~: les représentations pyramidales

BGM2020 (Article (Journal)): Counting Phylogenetic Networks of Level 1 and 2

BhabakMukhopadhyay2014 (Misc): A 3-factor approximation algorithm for a Minimum Acyclic Agreement Forest on k rooted, binary phylogenetic trees

BMD2004 (InProceedings): Une nouvelle méthode pour la détection de transferts horizontaux de gène : la réconciliation topologique d'arbres de gène et d'espèces

Bryant1997 (PhdThesis): Building Trees, Hunting for Trees, and Comparing Trees: theory and method in phylogenetic analysis

Byrka2008 (PhdThesis): Randomized Approximation Algorithms: Facility Location, Phylogenetic Networks, Nash Equilibria

Cecchetti2007 (Article (Journal)): Orientability of Phylogenetic Network Graphs

CLRV2008e (InProceedings): Phylogenetic Networks: Justification, Models, Distances and Algorithms

CMF2010 (Misc): A metric for galled networks

Collins2009 (MastersThesis): Rekernelisation Algorithms in Hybrid Phylogenies

DHKSM2012 (Book): An Introduction to Phylogenetic Combinatorics

EslahchiHassanzadeh2011 (InProceedings): New Algorithm for Constructing Supernetworks from Partial Trees

ExcoffierSmouse1994 (Article (Journal)): Using Allele Frequencies and Geographic Subdivision to Reconstruct Gene Trees Within a Species: Molecular Variance Parsimony

FGM2019 (Article (Journal)): Counting Phylogenetic Networks with Few Reticulation Vertices: Tree-Child and Normal Networks

FHS2020 (Misc): Normalising phylogenetic networks

ForceyScalzo2020 (Misc): Phylogenetic networks as circuits with resistance distance

ForceyScalzo2020b (Misc): Galois connections for phylogenetic networks and their polytopes

FRY2020 (Misc): On the Asymptotic Growth of the Number of Tree-Child Networks

Gauthier2006 (PhdThesis): Utilisation de réseaux en analyse phylogénétique

Gemeinholzer2008 (InBook): Phylogenetic networks

GIJJLM2020 (Misc): Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes

GLZ2016 (InProceedings): A program for verification of phylogenetic network models

Gorecki2003 (InProceedings): Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model

Gorecki2006 (PhdThesis): Detection of horizontal gene transfer

Grant1971 (InBook): Plant Speciation

GrasslyRambaut1999 (Misc): Treevolve, a program to simulate the evolution of DNA sequences under different population dynamic scenarios

Graur2016 (InBook): Reticulate evolution and phylogenetic networks

GunawanZhang2015 (Misc): Bounding the Size of a Network Defined By Visibility Property

Gusfield2005 (Misc): On the Full-Decomposition Optimality Conjecture for Phylogenetic Networks

Gusfield2014 (Book): ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks

GusfieldHickerson2004 (Misc): A Fundamental, Efficiently-Computed Lower Bound on the Number of Recombinations Needed in Phylogenetic Networks

HallettLagergren2004 (Misc): Efficient algorithms for lateral gene transfers problems

HHJS2005 (InProceedings): Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets

HIJJMMS2019 (Misc): Rooting for phylogenetic networks

HLM2020 (Misc): Weakly displaying trees in temporal tree-child network

HLPM2002 (Article (Journal)): Spectronet: A package for computing spectra and median networks

HMW2019 (Article (Journal)): Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks

Holland2001 (PhdThesis): Evolutionary analyses of large data sets: Trees and beyond

HRS2011 (Book): Phylogenetic Networks: Concepts, Algorithms and Applications

HSW2005 (InBook): The coalescent with recombination

Humphries1983 (InProceedings): Primary data in hybrid analysis

Huson2007a (InBook): Split networks and Reticulate Networks

HusonWetzel1995 (Misc): Analyzing and visualizing sequence and distance data with SplitsTree V1.0.2

Iersel2009 (PhdThesis): Algorithms, Haplotypes and Phylogenetic Networks

IerselKelk2009 (Misc): A short note on the tractability of constructing phylogenetic networks from clusters

IerselScornavaccaKelk2014 (Misc): Exact reconciliation of undated trees

IKLS2013 (Misc): A short note on exponential-time algorithms for hybridization number

JanssonSung2008 (InBook): The Maximum Agreement of Two Nested Phylogenetic Networks

Jetten2015 (Misc): Characterising tree-based phylogenetic networks

KececiogluGusfield1994 (InProceedings): Reconstructing a history of recombinations from a set of sequences

Kelk2011 (Misc): A note on efficient computation of hybridization number via softwired clusters

KelkScornavacca2012 (Misc): Towards the fixed parameter tractability of constructing minimal phylogenetic networks from arbitrary sets of nonbinary trees

KlawitterStumpf2020 (Misc): Drawing Tree-Based Phylogenetic Networks with Minimum Number of Crossings

KLM2013 (Misc): Fighting network space: it is time for an SQL-type language to filter phylogenetic networks

Kloepper2008 (PhdThesis): Algorithms for the Calculation and Visualisation of Phylogenetic Networks

KPMG2017 (Article (Journal)): Intertwining phylogenetic trees and networks

KusherbaevaVyahhi2008 (InProceedings): Stochastic Approach to Binary Matrix Partitioning for Phylogenetic Networks

Labarre2008 (PhdThesis): Combinatorial aspects of genome rearrangements and haplotype networks

Lekic2015 (PhdThesis): Trees, agreement forests and treewidth: combinatorial algorithms for constructing phylogenetic networks

Lesser2007 (PhdThesis): Optimal and Hereditarily Optimal Realizations of Metric Spaces

Linz2008 (PhdThesis): Reticulation in evolution

LMNW2004 (InProceedings): Network (Reticulate) Evolution: Biology, Models, and Algorithms

Lott2009 (PhdThesis): New Methods for Constructing Phylogenetic Networks from Multi-Labelled Trees

LyubetskyVyugin2003 (Article (Journal)): Methods of horizontal gene transfer determination using phylogenetic data

Mansouri2020 (PhdThesis): Combinatorial properties of phylogenetic networks

Mansouri2020b (Misc): Counting General Phylogenetic networks

Mitchell2016 (PhdThesis): Distinguishing Convergence on Phylogenetic Networks

MNW2002 (Misc): An error metric for phylogenetic networks

Morgado2015 (MastersThesis): Propriétés structurelles et relations des classes de réseaux phylogénétiques

Morin2007 (PhdThesis): Phylogenetic Networks: Simulation, Characterization, and Reconstruction

Morrison2010b (InBook): Phylogenetic networks in systematic biology (and elsewhere)

Morrison2011 (Book): Introduction to Phylogenetic Networks

Morrison2013 (InBook): Phylogenetic networks are fundamentally different from other kinds of biological networks

MoultonHuber2005 (InBook): Phylogenetic Networks

MyersGriffiths2003 (Article (Journal)): Bounds on the Minimum Number of Recombination Events in a Sample History

Nakhleh2004 (PhdThesis): Phylogenetic Networks

Nakhleh2017 (Misc): Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees

NBM2005 (InProceedings): HGT-Simulator : logiciel pour simuler des transferts horizontaux

Nelson1983 (InProceedings): Reticulation in Cladograms

Nguyen2010 (PhdThesis): Novel Split-Based Approaches to Computing Phylogenetic Diversity and Planar Split Networks

Nguyen2013 (PhdThesis): Réconciliations: corriger des arbres de gènes et inférer la fiabilité des événements évolutifs

Phipps2011 (PhdThesis): Planar phylogenetic network optimization

Radice2011 (PhdThesis): A Bayesian Approach to Phylogenetic Networks

Rea2011 (PhdThesis): Statistical approaches to phylogenetic networks, recombination and testing of incongruence

RiesebergMorefield1995 (InBook): Character expression, phylogenetic reconstruction, and the detection of reticulate evolution

Rohl1999 (PhdThesis): Phylogenetische Netzwerke

Ruths2005 (MastersThesis): Applications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer

SchierupHein2000a (Article (Journal)): Consequences of recombination on traditional phylogenetic analysis

Schliep2009 (PhdThesis): Some applications of statistical phylogenetics

Scholz2018 (PhdThesis): New algorithms and mathematical tools for phylogenetics beyond trees

Scornavacca2017 (Misc): Occam's razor in phylogenetic network reconstruction

Semple2007 (InBook): Hybridization Networks

SLL2005 (InProceedings): Efficient Algorithms for Constructing Phylogenetic Networks with Restricted Recombinations

SolisLemus2015 (PhdThesis): Statistical methods to infer population structure with coalescence and gene flow

Sonke2013 (Misc): Reconstructing a level-1-network from quartets

Steel2016 (InBook): Introduction to phylogenetic networks

TCS1992 (Article (Journal)): A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation

TEPA2011 (Misc): TripNet: A Method for Constructing Phylogenetic Networks from Triplets

Than2010 (PhdThesis): Inference of parsimonious species phylogenies from multi-locus data

To2011 (PhdThesis): On some graph problems in phylogenetics

Tofigh2009 (PhdThesis): Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression

TSSAL2009 (Misc): Detecting LGTs using a novel probabilistic model integrating duplications, LGTs, losses, rate variation, and sequence evolution

TullerSnir2007 (Misc): The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks

Venugopal2009 (MastersThesis): Improving layout of phylogenetic network produced by PADRE

VenugopalBereg2009 (InProceedings): Layout of Phylogenetic Networks and Multi-Labeled Trees

Voorkamp2014 (PhdThesis): Untangling Evolution

Vriesendorp2007 (PhdThesis): Phylogenenetworks, exploring reticulate evolution and its consequences for phylogenetic reconstruction

Wagner1983 (InProceedings): Reticulistics: the recognition of hybrids and their role in cladistics and classification

Wanntorp1983 (InProceedings): Reticulated cladograms and the identification of hybrid taxa

Wen2016 (MastersThesis): Bayesian Inference of Phylogenetic Networks

Wen2017 (PhdThesis): Bayesian Inference of Phylogenetic Networks from Sequence Data

Wetzel1995 (PhdThesis): Zur Visualisierung abstrakter Ahnlichkeitsbeziehungen

Wicke2016 (MastersThesis): Extending the concept of phylogenetic diversity and its measures from trees to networks

Wu2009 (PhdThesis): Phylogenetic Networks: New Constructions and Applications

Wu2016 (PhdThesis): Quartet weights in phylogenetic network reconstruction

YuNakhleh2012 (Misc): Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting

ZBB2007 (Misc): Optimizing Split Networks

ZDE2013 (Misc): Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees

ZDS2011 (Misc): Probabilistic modeling of gene trees given species networks

Zhang2007 (PhdThesis): Optimization Algorithms for Phylogenetic Networks

Zhu2013 (PhdThesis): Stochastic tree models and probabilistic modelling of gene trees of given species networks

ZMJ2004 (Article (Journal)): Use of Phylogenetic network and its reconstruction Algorithms

## Not yet tagged by keywords (67 references)

AEUV2006: Site Consistency in Phylogenetic Networks with Recombination

Albrecht2016: Computing Hybridization Networks Using Agreement Forests

Bandelt1994: Phylogenetic Networks

BandeltDress1994: An order theoretic framework for overlapping clustering

BaoBereg2009: Counting Faces in Split Networks

BeikoRagan2009: Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction

BeregZhang2005: Phylogenetic Networks Based on the Molecular Clock Hypothesis

BeregZhang2006: Phylogenetic Networks Based on the Molecular Clock Hypothesis

BertrandDiday1990: Une généralisation des arbres hiérarchiques~: les représentations pyramidales

BGET2008: Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion

BloomquistSuchard2010: Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework

BMD2004: Une nouvelle méthode pour la détection de transferts horizontaux de gène : la réconciliation topologique d'arbres de gène et d'espèces

BocMakarenkov2003: New Efficient Algorithm for Detection of Horizontal Gene Transfer Events

BPM2010: Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity

Bryant1997: Building Trees, Hunting for Trees, and Comparing Trees: theory and method in phylogenetic analysis

Bryant2004: The Splits in the Neighborhood of a Tree

Byrka2008: Randomized Approximation Algorithms: Facility Location, Phylogenetic Networks, Nash Equilibria

CLRV2011: Comparison of Galled Trees

DezulianSteel2004: Phylogenetic closure operations and homoplasy-free evolution

DHM1997: Some Variations on a Theme by Buneman

Doolittle1999: Phylogenetic Classification and the Universal Tree

ELNR2003: Reconstructing the evolutionary history of Indo-European languages using answer set programming

ELR2006: Temporal phylogenetic networks and logic programming

Gauthier2006: Utilisation de réseaux en analyse phylogénétique

GauthierLapointe2002: A comparison of alternative methods for detecting reticulation events in phylogenetic analysis

GHE2007: An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study

GKL2009: Quartets in maximal weakly compatible split systems

GusfieldHickerson2004: A Fundamental, Efficiently-Computed Lower Bound on the Number of Recombinations Needed in Phylogenetic Networks

Hein1990: Reconstructing evolution of sequences subject to recombination using parsimony

HHJS2005: Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets

HHJS2006: Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets

HMS2004: Replacing cliques by stars in quasi-median graphs

HSW2005: The coalescent with recombination

HudsonKaplan1985: Statistical Properties of the Number of Recombination Events in the History of a Sample of DNA Sequences

IKKSHB2009: Constructing Level-2 Phylogenetic Networks from Triplets

ISS2010: Quantifying the Extent of Lateral Gene Transfer Required to Avert a 'Genome of Eden'

KGDO2005: The net of life: Reconstructing the microbial phylogenetic network

KNX2006: Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms

Legendre2000a: Reticulate evolution: From bacteria to philosophers

Legendre2000b: Biological Applications of Reticulate Analysis

LMNW2004: Network (Reticulate) Evolution: Biology, Models, and Algorithms

LyubetskyVyugin2003: Methods of horizontal gene transfer determination using phylogenetic data

MBDDP2006: New Efficient Algorithm for Modeling Partial and Complete Gene Transfer Scenarios

McBreenLockhart2006: Reconstructing reticulate evolutionary histories of plants

MLD2004: Modeling phylogenetic relationships using reticulated networks

MoultonHuber2005: Phylogenetic Networks

NBM2005: HGT-Simulator : logiciel pour simuler des transferts horizontaux

PJMCBG2009: Minimizing recombinations in consensus networks for phylogeographic studies

Poptsova2009: Testing Phylogenetic Methods to Identify Horizontal Gene Transfer

PosadaCrandall2002: The effect of recombination on the accuracy of phylogeny estimation

RKMJ2007: Parallel Construction of Conflict Graph for Phylogenetic Network Problem

Rohl1999: Phylogenetische Netzwerke

Rohlf2000: Phylogenetic models and reticulations

RuthsNakhleh2005: Recombination and phylogeny: effects and detection

SchierupHein2000a: Consequences of recombination on traditional phylogenetic analysis

SchierupHein2000b: Recombination and the molecular clock

Smouse2000: Reticulation inside the species boundary

Sneath2000: Reticulate Evolution in Bacteria and Other Organisms: How Can We Study It?

TrujilloCotta2006: An Evolutionary Approach to the Inference of Phylogenetic Networks

VDJPPW2010: Beyond evolutionary trees

VriesendorpBakker2005: Reconstructing patterns of reticulate evolution in angiosperms: what can we do?

WuGusfield2006: Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes)

WuGusfield2007a: Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes)

WuGusfield2007b: Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants

ZBB2007: Optimizing Split Networks

ZMJ2005a: A Classification Based Approach for Root Unknown Phylogenetic Networks under Constrained Recombination

ZMJ2006: A pattern recognition-based approach for phylogenetic network construction with constrained recombination

## Keywords not yet defined (124 keywords)

agreement forestancestral trait reconstruction

APX hard

ARG

bayesian

bootstrap

bound

branch length

characterization

cherry-picking

cluster containment

clustering

compression

consensus

cophylogeny

counting

database

display set

distance between networks

distinguishability

diversity

duplication

dynamic programming

enumeration

exponential algorithm

from binary characters

from continuous characters

from distances

from gene order

from multistate characters

from NGS data

from quarnets

from quartets

from rooted trees

from sequences

from splits

from subnetworks

from trees

from tri-LGT-nets

from trinets

from triplets

from unrooted trees

generation

heuristic

History bound

HMM

hybridization

identifiability

inapproximability

incomplete lineage sorting

integer linear programming

isomorphism

kth-order reduced network

lateral gene transfer

LGT network

likelihood

lineage sorting

loss

LST distance

MedianJoining

minimal lateral network

minimum contradiction

minimum number

minimum spanning network

model selection

MSOL

mu distance

netting

NNI distance

NNI moves

number of vertices

orchard network

orientation

outerplanar

parental hybridization

parsimony

partly reduced networks

pedigree

perfect

phylogeny

planar

polynomial

population genetics

Program ARTNET

Program FlatNJ

Program HiDe

Program Hybrid-coal

Program IcyTree

Program IGNet

Program lingpy

Program MaafB

Program Notung

Program PhyloSketch

Program Quartet Decomposition

Program QuartetNet

Program QuickCass

Program SylvX

Program TCGenerators

pseudo-polynomial

quasi-reticulation-visible network

recombination

recombination detection

reduced networks

rigidly displaying

SAT

semidirected network

serial evolutionary networks

simulated annealing

site consistency

split

spread

statistical test

survey

TBR distance

temporal-hybridization number

time consistent network

tree containment

tree-child network

tree-child sequence

uniqueness

unrooted tree-based network

valid network

visualization

weakly displaying

## Citations

This website was cited in some publications [KusherbaevaVyahhi2008, Iersel2008, ToHabib2009, Berry2009, LSHM2009, Bao2009, Nakhleh2010, IKRH2010, HIKS2010, To2011, HRS2011, Morrison2011, BBBDDDLRV2012, HabibTo2012, HusonScornavacca2012, LabarreVerwer2013] and on those websites [1, 2, 3, 4, 5, 6, 7, 8, 9]: thank you!