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 and Sylvain Guillemot 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 368 references by 346 authors.There are 148 keywords and 1846 keyword-publication associations.

Missing URL (22 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
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
BloomquistSuchard2010: Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework
DHM2001: Hereditarily Optional Realizations: Why are they Relevant in Phylogenetic Analysis, and how does one Compute them?
GauthierLapointe2002: A comparison of alternative methods for detecting reticulation events in phylogenetic analysis
Gorecki2006: Detection of horizontal gene transfer
Grant1971: Plant Speciation
HSW2005: The coalescent with recombination
Humphries1983: Primary data in hybrid analysis
Morrison2010b: Phylogenetic networks in systematic biology (and elsewhere)
MoultonHuber2005: Phylogenetic Networks
Nelson1983: Reticulation in Cladograms
PJN2010b: Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees
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 (82 references)

AEUV2006: Site Consistency in Phylogenetic Networks with Recombination
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
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
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
HumphriesSemple2009: Note on the hybridization number and subtree distance in phylogenetics
IKKSHB2009: Constructing Level-2 Phylogenetic Networks from Triplets
ISS2010: Quantifying the Extent of Lateral Gene Transfer Required to Avert a 'Genome of Eden'
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
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
PJN2010b: Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees
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?
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
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
Willson2010b: Properties of normal phylogenetic networks
Willson2010c: Relationships Among 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 (51 keywords)

APX hard
ARG
bootstrap
bound
characterization
clustering
consensus
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
integer linear programming
lateral gene transfer
likelihood
lineage sorting
MedianJoining
minimum number
minimum spanning network
model selection
mu distance
netting
parsimony
perfect
phylogeny
polynomial
Program MPR
recombination
recombination detection
serial evolutionary networks
simulated annealing
site consistency
split
survey
time consistent network
triplet distance
visualization


Coauthor graph

Coauthor graphs computed from the database are available here.

Source code

Here is some code I've added to BibAdmin to implement new functionalities: PHP code.


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!