Introduction

SERAPHIM ("Studying Environmental Rasters and PHylogenetically Informed Movements") is a suite of computational methods developed to study phylogenetic reconstructions of spatial movement in an environmental context. SERAPHIM extracts the spatio-temporal information contained in estimated phylogenetic trees and uses this information to calculate summary statistics of spatial spread and to visualize dispersal history. Most importantly, SERAPHIM enables users to study the impact of customized environmental variables on the spread of the study organism. Specifically, given an environmental raster, SERAPHIM computes environmental "weights" for each phylogeny branch, which represent the degree to which the environmental variable impedes (or facilitates) lineage movement. Correlations between movement duration and these environmental weights are then assessed, and the statistical significances of these correlations are evaluated using null distributions generated by a randomization procedure. SERAPHIM can be applied to any phylogeny whose nodes are annotated with spatial and temporal information. At present, such phylogenies are most often found in the field of emerging infectious diseases, but will become increasingly common in other biological disciplines as population genomic data grows.SERAPHIM 1.0 is freely available from http://evolve.zoo.ox.ac.uk/ R package, source code, example files, tutorials and a manual are also available from this website.simon.dellicour@kuleuven.be or oliver.pybus@zoo.ox.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.

Publications

  1. SERAPHIM: studying environmental rasters and phylogenetically informed movements.
    Cite this
    Dellicour S, Rose R, Faria NR, Lemey P, Pybus OG, 2016-10-01 - Bioinformatics (Oxford, England)
  2. Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data.
    Cite this
    Dellicour S, Rose R, Pybus OG, 2016-02-01 - BMC bioinformatics
  3. Phylogeography takes a relaxed random walk in continuous space and time.
    Cite this
    Lemey P, Rambaut A, Welch JJ, Suchard MA, 2010-08-01 - Molecular biology and evolution

Credits

  1. Simon Dellicour
    Developer

    Department of Microbiology and Immunology, Rega Institute for Medical Research, Belgium

  2. Rebecca Rose
    Developer

    BioInfoExperts LLC, Norfolk

  3. Nuno R Faria
    Developer

    Department of Zoology, University of Oxford

  4. Philippe Lemey
    Developer

    Department of Microbiology and Immunology, Rega Institute for Medical Research, Belgium

  5. Oliver G Pybus
    Investigator

    Department of Zoology, University of Oxford

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT001687
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByOliver G Pybus