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)
How should we treat hybrids in a taxonomic scheme?

Can networks have multiple roots?
Time inconsistency in evolutionary networks
Networks and most recent common ancestors
Another phylogenetic network outside science

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
Releasing phylogenetic data

Biological versus phylogenetic networks
Network measures and phylogenetic networks

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

Reviews of recent books
RECOMB-AB

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

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

EDA or post-optimality analysis of phylogenetic data?
Some possible questions for EDA in phylogenetics
Representing evolutionary scenarios using splits graphs

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?

Distortions and artifacts in Principal Components Analysis analysis of genome data
Networks can outperform PCA ordinations in phylogenetic analysis

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?

First-degree relationships and partly directed networks
Cophylogenetic networks