TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories

Research output: Contribution to journalArticle

Open Access permissions





Organisational units


Phylogenetic networks are a generalisation of evolutionary trees that can be used to represent reticulate processes such as hybridisation and recombination. Here we introduce a new approach called TriLoNet to construct such networks directly from sequence alignments which works by piecing together smaller phylogenetic networks. More specifically, using a bottom up approach similar to Neighbor-Joining, TriLoNet constructs level-1 networks (networks that are somewhat more general than trees) from smaller level-1 networks on three taxa. In simulations we show that TriLoNet compares well with Lev1athan, a method for reconstructing level-1 networks from three-leaved trees. In particular, in simulations we find that Lev1athan tends to generate networks that overestimate the number of reticulate events as compared with those generated by TriLoNet. We also illustrate TriLoNet’s applicability using simulated and real sequence data involving recombination, demonstrating that it has the potential to reconstruct informative reticulate evolutionary histories. TriLoNet has been implemented in JAVA and is freely available at https://www.uea.ac.uk/computing/TriLoNet.


Original languageEnglish
Pages (from-to)2151-2162
Number of pages12
JournalMolecular Biology and Evolution
Issue number8
Early online date15 Apr 2016
Publication statusPublished - Aug 2016


    Research areas

  • Phylogenetic network, reticulate evolution, networks reconstruction, supernetwork

View graph of relations

ID: 74057108

Related by author
  1. Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks

    Research output: Contribution to journalArticle

  2. Quarnet Inference Rules for Level-1 Networks

    Research output: Contribution to journalArticle

  3. UPGMA and the normalized equidistant minimum evolution problem

    Research output: Contribution to journalArticle

  4. Bounds for phylogenetic network space metrics

    Research output: Contribution to journalArticle

  5. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution

    Research output: Contribution to journalArticle