Phylogenetic Networks: Algorithms and applications

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popart: full‐feature software for haplotype network construction (2015, methodology): “This method, described in detail in Bandelt, Forster & R € ohl (1999) and Huson, Rupp & Scornavacca (2011), includes nodes to represent inferred (unsampled) sequences by iteratively adding ‘median’ sequence vectors when these nodes shorten the total length of the network.”
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data (2012, methodology): “Graph-based models are of growing interest in phylogenetics [45,46], but have been rarely used in population genetics (with some exceptions [37,40,47]).”
Topology of viral evolution (2013, background): “Although some of these methods cease to be NP-hard (19), all prioritize computational tractability over biological modeling (20).”