Methodology

Some blog posts discussing the technical aspects of constructing phylogenetic networks

A fundamental limitation of hybridization networks?
A fundamental limitation of hybridization networks? (2)
A fundamental limitation of pedigrees and networks but not trees
A limitation of turning splits graphs into reticulate networks
The practical limits of networks?

Arguments against the use of networks?

How should we treat hybrids in a taxonomic scheme?
Monophyletic groups in networks
On partitioning incongruent data into congruent blocks

Can networks have multiple roots?
Time inconsistency in evolutionary networks
Networks and most recent common ancestors
Is rate variation among lineages actually due to reticulation?
Rate variation and gene tree discordance
Reconstructing ancestors in a splits network?
Current methods for evolutionary networks
Networks vs augmented trees

Are genotype or phenotype data more tree-like?
Using networks, not trees, to display hybrids
Is phylogenomics tree-like?
Is the Ring of Life a network?
Hybridization in the world of duplication-transfer-loss

Does it matter which way up a tree is drawn?
"Basal" and "crown" are dirty words in phylogenetics

Inconsequential splits in NeighborNet graphs

Another phylogenetic network outside science
The phylogenetics of Little Red Riding Hood
Roots and the phylogenetics of mythology
Candy Crush network
A network of cheese rind microorganisms?
Guitars and networks
Networks of music history
Network of Linné's "Philosophia Botanica" editions 

Validating methods for constructing evolutionary phylogenetic networks
What should a database of datasets look like?
GPWG Poaceae dataset
Datasets for validating algorithms for evolutionary networks
More datasets for validating network algorithms
Request for datasets
Is this a "gold standard" dataset?
Some new additions to the dataset database

Poor bioinformatics?
Releasing phylogenetic data
Public availability of phylogenetic data
Archiving of bioinformatics software
Archiving of phylogenetics data
Biological versus phylogenetic networks
Network measures and phylogenetic networks
Trees, treemaps and networks
Circular phylograms for phylogenetic networks

Complicated network visualizations
GeneaQuilts

Are mathematical constraints biologically realistic?
Different topological restrictions of rooted phylogenetic networks. Which make biological sense?
Topological restrictions: some comments
Are realistic mathematical models necessary?

Network thinking in phylogeography?

Reviews of recent books
Recent book reviews
RECOMB-AB
Report from conference Mathematical and Computational Evolutionary Biology 2013 (MCEB 2013)

An update on level-k phylogenetic networks
New version of phylogenetic networks software

Networks and bootstraps as tree-support criteria
Rooted networks for exploratory data analysis
When is there support for a large phylogeny?

Human races, networks and fuzzy clusters
Admixture graphs – evolutionary networks for population biology
Using phylogenetic analyses for textual analysis
Complex hybridizations in wheat
Complex hybridizations in barley and its relatives
Grape genealogies are networks, not trees
Tardigrades and phylogenetic networks
The network of woodpeckers, etc
Networks of admixture or introgression
Y chromosome and mitochondrial DNA phylogenies — networks?

Problems with manually constructing networks
Are networks actually used to explore reticulate histories?
Studying gene flow using genomes

Uses of MUL-trees for evolutionary networks

Open questions about evolutionary networks, part 1
Open questions about evolutionary networks, part 2
Open questions about evolutionary networks, part 3
An open question about computational complexity
Using constraints to get a handle on the space of phylogenetic networks?
Phylogenetic network Millennium problems
Open problems in phylogenetics
First millennium problem has been solved: tree containment is easy on stable networks

EDA or post-optimality analysis of phylogenetic data?
Tree Alignment Graphs and data-display networks
Some possible questions for EDA in phylogenetics
Representing evolutionary scenarios using splits graphs
Using data-display networks to assess evolutionary inferences
Why do so few biologists look at their phylogenetic data?

Some things you probably don't know about the bootstrap

Non-model distances in phylogenetics
Phylogenetics of computer viruses?

Are phylogenetic networks as scientific as trees?
Description, explanation and prediction in phylogenetics
Is there a philosophy of phylogenetic networks?

Are phylogenetic trees useful for domesticated organisms?
Domestication networks are complicated
Networks and human inter-population variation
Network of apple cultivars
The phylogenetics of angiosperm classification schemes

Distortions and artifacts in Principal Components Analysis analysis of genome data
Networks can outperform PCA ordinations in phylogenetic analysis
Continued misuse of PCA in genomics studies
Pacific rock art - ordinations and networks
Phylogenetic networks as multivariate data displays

We should present bayesian phylogenetic analyses using networks
Cloudograms and data-display networks
Pasta have no phylogeny (so don't try to give them one)
Should phylogenetic modelling proceed from simple to complex or vice versa?

Resistance to network thinking
Destroying the Tree of Life?
A rant about the term "evolutionary network"
Phylogenetic networks and "evolutionary networks"

First-degree relationships and partly directed networks
Cophylogenetic networks

Conflicting placental roots: network or tree?
Why are there conflicting placental roots?
Network of Australian marsupials
Conflicting avian roots

Checking data errors with phylogenetic networks
Multivariate data displays are not always necessary

Barcodes, metaphors, and phylogenetic networks
Next Generation Sequencing and phylogenetic networks
Phylogenomics: the effect of data quality on sampling bias
Phylogenetics, ecologist style
The Phylocode and reticulation

Evolution and timelines
Evolution and timelines, 2
Non-phylogenetic trees

Reducing networks to trees
Networks to detect ancient recombinations
Producing trees from datasets with gene flow
Representing macro- and micro-evolution in a network
Darwin's Finches, genomics and phylogenetic networks

Uncertainty in multiple sequence alignments
The need for a new sequence alignment database
The need for a new sequence alignment program