L.U.St: a tool for approximated maximum likelihood supertree reconstruction

• Published in: BMC bioinformatics Vol. 15; no. 1; p. 183
• Main Authors: Akanni, Wasiu A, Creevey, Christopher J, Wilkinson, Mark, Pisani, Davide
• Format: Journal Article
• Language: English
• Published: London BioMed Central 12.06.2014; BioMed Central Ltd; Springer Nature B.V
• Subjects: Algorithms; Animals; Bioinformatics; Biomedical and Life Sciences; Colleges & universities; Comparative genomics; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Genomics; Humans; Hypotheses; Life Sciences; Likelihood Functions; Methods; Microarrays; Phylogenetics; Phylogeny; Programming languages; Python; Software; Trees; Maximum likelihood; Supertrees; Tests of two trees; Phylogenomics
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-15-183

Background Supertrees combine disparate, partially overlapping trees to generate a synthesis that provides a high level perspective that cannot be attained from the inspection of individual phylogenies. Supertrees can be seen as meta-analytical tools that can be used to make inferences based on results of previous scientific studies. Their meta-analytical application has increased in popularity since it was realised that the power of statistical tests for the study of evolutionary trends critically depends on the use of taxon-dense phylogenies. Further to that, supertrees have found applications in phylogenomics where they are used to combine gene trees and recover species phylogenies based on genome-scale data sets. Results Here, we present the L.U.St package, a python tool for approximate maximum likelihood supertree inference and illustrate its application using a genomic data set for the placental mammals. L.U.St allows the calculation of the approximate likelihood of a supertree, given a set of input trees, performs heuristic searches to look for the supertree of highest likelihood, and performs statistical tests of two or more supertrees. To this end, L.U.St implements a winning sites test allowing ranking of a collection of a-priori selected hypotheses, given as a collection of input supertree topologies. It also outputs a file of input-tree-wise likelihood scores that can be used as input to CONSEL for calculation of standard tests of two trees (e.g. Kishino-Hasegawa, Shimidoara-Hasegawa and Approximately Unbiased tests). Conclusion This is the first fully parametric implementation of a supertree method, it has clearly understood properties, and provides several advantages over currently available supertree approaches. It is easy to implement and works on any platform that has python installed. Availability: bitBucket page - mailto:afro-juju@bitbucket.org/afro-juju/l.u.st.git. Contact: Davide.Pisani@bristol.ac.uk.