3 Works

Data from: Maximum likelihood inference of small trees in the presence of long branches

Nick Goldman & Sarah L. Parks
The statistical basis of maximum likelihood (ML), its robustness and the fact that it appears to suffer less from biases lead to it being one of the most popular methods for tree reconstruction. Despite its popularity, very few analytical solutions for ML exist, so biases suffered by ML are not well understood. One possible bias is long branch attraction (LBA), a regularly-cited term generally used to describe a propensity for long branches to be joined...

Data from: Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

Ge Tan, Manuel Gil, Ari P. Löytynoja, Nick Goldman & Christophe Dessimoz
Multiple sequence aligners typically work by progressively aligning the most closely related sequences or group of sequences according to guide trees. In PNAS, Boyce et al. report that alignments reconstructed using simple chained trees (i.e., comb-like topologies) with random leaf assignment performed better in protein structure-based benchmarks than those reconstructed using phylogenies estimated from the data as guide trees. The authors state that this result could turn decades of research in the field on its...

Data from: Cuckoo hosts shift from accepting to rejecting parasitic eggs across their lifetime

Mercedes Molina-Morales, David Martín-Gálvez, Deborah A. Dawson, Terry A. Burke, Jesús Miguel Avilés & Juan Gabriel Martínez
One of the best known outcomes of coevolution between species is the rejection of mimetic parasite eggs by avian hosts, which has evolved to reduce costly cuckoo parasitism. How this behavioral adaptation varies along the life of individual hosts remains poorly understood. Here we identify for the first time, lifetime patterns of egg rejection in a parasitized long-lived bird, the magpie Pica pica and show that, during the years they were studied, some females accept,...

Registration Year

  • 2014

Resource Types

  • Dataset


  • European Bioinformatics Institute
  • University of Zurich
  • Spanish National Research Council
  • University of Helsinki
  • Imperial College London
  • University of Granada
  • University of Sheffield