About the Who's Who of Phylogenetic Networks

This website is a database of articles about phylogenetic networks administrated by Philippe Gambette.

Josh Collins, Leo van Iersel, David Morrison also contributed to the database.

The decision to include or not an article in the database is sometimes tough, especially for the ones which deal with recombination detection, which implicitly produce recombination networks. If you are interested in this topic, you may check this list of programs dedicated to recombination detection.


Articles or topics which may one day be in the database


You can help to build the Who's Who of Phylogenetic Networks!

If you are cited in the database, you can contact me to modify any information concerning you (homepage, photo), your articles (mistakes in the citation, update, additional material...) or your programs. Any suggestion is also welcome.

You can also register ("Login" Button on any page of the Who's Who) to get the rights to modify the database yourself. Then, after logging in, you can suggest new keywords, or better definitions, and relations between articles and keywords. The database currently contains 342 references by 317 authors.There are 135 keywords and 1510 keyword-publication associations.

Missing URL (27 references)

AEUV2006: Site Consistency in Phylogenetic Networks with Recombination
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
Bertrand1986: Étude de la représentation pyramidale
BertrandDiday1985: A visual representation of the compatibility between an order and a dissimilarity index: the pyramids
BryantMoulton2002: Neighbor-Net: An Agglomerative Method for the Construction of Planar Phylogenetic Networks
DHM2001: Hereditarily Optional Realizations: Why are they Relevant in Phylogenetic Analysis, and how does one Compute them?
DressHuson2004: Constructing splits graphs
Dubrova2005: Phylogenetic networks with edge-disjoint recombination cycles
GauthierLapointe2002: A comparison of alternative methods for detecting reticulation events in phylogenetic analysis
Gorecki2006: Detection of horizontal gene transfer
Grant1971: Plant Speciation
HHJS2005: Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets
HSW2005: The coalescent with recombination
Humphries: Primary data in hybrid analysis
Huson2003: What If I Don't Have a Tree? Split Decomposition and Related Models
JNS2005: Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network
KececiogluGusfield1994: Reconstructing a history of recombinations from a set of sequences
Lapointe2000: How to account for reticulation events in phylogenetic analysis: A review of distance-based methods
MoultonHuber2005: Phylogenetic Networks
Nelson1983: Reticulation in Cladograms
Sung2008: Constructing a Galled Phylogenetic Network
Wagner1983: Reticulistics: the recognition of hybrids and their role in cladistics and classification
Wanntorp1983: Reticulated cladograms and the identification of hybrid taxa
Wetzel1995: Zur Visualisierung abstrakter Ahnlichkeitsbeziehungen


Not yet tagged by keywords (93 references)

AEUV2006: Site Consistency in Phylogenetic Networks with Recombination
AylingBrown2009: Novel methodology for construction and pruning of quasi-median networks
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
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
CLRV2010b: Comparison of Galled Trees
Collins2009: Rekernelisation Algorithms in Hybrid Phylogenies
DezulianSteel2004: Phylogenetic closure operations and homoplasy-free evolution
DHM1997: Some Variations on a Theme by Buneman
DHM2001: Hereditarily Optional Realizations: Why are they Relevant in Phylogenetic Analysis, and how does one Compute them?
Doolittle1999: Phylogenetic Classification and the Universal Tree
Dubrova2005: Phylogenetic networks with edge-disjoint recombination cycles
ELNR2003: Reconstructing the evolutionary history of Indo-European languages using answer set programming
ELR2006: Temporal phylogenetic networks and logic programming
FischerHuson2009: New Common Ancestor Problems in Trees and Directed Acyclic Graphs
GambetteHuber2009: A Note on Encodings of Phylogenetic Networks of Bounded Level
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
HIKS2010: A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks
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
HumphriesSemple2009: Note on the hybridization number and subtree distance in phylogenetics
HusonRupp2010: Phylogenetic Networks
IKKSHB2009: Constructing Level-2 Phylogenetic Networks from Triplets
ISS2009: Quantifying the Extent of Lateral Gene Transfer Required to Avert a 'Genome of Eden'
JNST2007: On Approximating the Parsimony Score of Phylogenetic Networks
JNST2009: Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic
KGDO2005: The net of life: Reconstructing the microbial phylogenetic network
KNX2006: Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms
LeclercMakarenkov1998: On some relations between 2-trees and tree metrics
Legendre2000a: Special section on reticulate evolution
Legendre2000b: Biological Applications of Reticulate Analysis
LMNW2004: Network (Reticulate) Evolution: Biology, Models, and Algorithms
Lott2009: New Methods for Constructing Phylogenetic Networks from Multi-Labelled Trees
LSS2010: Analyzing and reconstructing reticulation networks under timing constraints
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
Nakhleh2009b: Evolutionary phylogenetic networks: models and issues
Nakhleh2010: A Metric on the Space of Reduced 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 reconstruction
RKMJ2007: Parallel Construction of Conflict Graph for Phylogenetic Network Problem
Rohl1999: Phylogenetische Netzwerke
Rohlf2000: Phylogenetic models and reticulations
RosselloValiente2009: All that Glisters is not Galled
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?
TCS1992: A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation
Tofigh2009: Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression
TrujilloCotta2006: An Evolutionary Approach to the Inference of Phylogenetic Networks
TSSAL2009: Detecting LGTs using a novel probabilistic model integrating duplications, LGTs, losses, rate variation, and sequence evolution
Valiente2009: Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R
VDJPPW2010: Beyond evolutionary trees
VelascoSober2009: Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection
VriesendorpBakker2005: Reconstructing patterns of reticulate evolution in angiosperms: what can we do?
WBLHM2005: Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths
WCHS2008: Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees
Willson2006b: Unique Reconstruction of Tree-Like Phylogenetic Networks from Distances Between Leaves
Willson2007c: Reconstruction of Some Hybrid Phylogenetic Networks with Homoplasies from Distances
Willson2010: Regular networks are determined by their trees
Willson2010b: Properties of normal phylogenetic networks
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 (48 keywords)

APX-hard
ARG
bootstrap
bound
characterization
clustering
consensus
construction
cophylogeny
distance between networks
diversity
duplication
enumeration
exponential algorithm
from distances
from quartets
from rooted trees
from sequences
from splits
from trees
from triplets
from unrooted trees
generation
heuristic
HMM
hybridization
inapproximability
lateral gene transfer
likelihood
lineage sorting
MedianJoining
minimum number
minimum spanning network
mu distance
netting
parsimony
perfect
phylogeny
polynomial
recombination
recombination detection
serial evolutionary networks
split
Splitstree
survey
time-consistent network
triplet distance
visualization


Coauthor graph


Citations

This website was cited in some publications [KusherbaevaVyahhi2008, Iersel2008, ToHabib2009, Berry2009, LSHM2009, Nakhleh2009, IKRH2009, HIKS2009] and on those websites [1, 2, 3, 4, 5, 6, 7]: thank you!