title: SERAPHIM: studying environmental rasters and phylogenetically informed movements.
abstract: 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.
authors.affiliation: Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Minderbroedersstaat 10, Leuven 3000, Belgium.
authors.forename: Simon
authors.initials: S
authors.lastname: Dellicour
authors.affiliation: BioInfoExperts LLC, Norfolk, Virginia, USA, 23518.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Rose
authors.affiliation: Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
authors.forename: Nuno R
authors.initials: NR
authors.lastname: Faria
authors.affiliation: Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Minderbroedersstaat 10, Leuven 3000, Belgium.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.affiliation: Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
mesh_terms: D019295:Computational Biology; D004777:Environment; D010802:Phylogeny; D011381:Programming Languages