Abstract
Networks are beginning to replace trees as the basic paradigm for data interpretation in phylogenetics. At the same time, next generation sequencing (NGS) offers the potential for generating suitable multilocus sequence data at a greater rate than ever before. Therefore, phylogeneticists now need to think about the relationship between NGS and phylogenetic networks, as there are a number of potential problems. These may not matter so much for tree-building algorithms, but it is a different matter for constructing networks. Each issue needs to be thought about to assess whether it is a serious problem or only of minor concern. Here, I introduce some of these issues, to start the discussion.
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