Dellicour S, Rose R, Pybus OG (2016) Explaining the geographic spread of emerging viruses: a new framework for comparing viral genetic information and environmental landscape data. BMC Bioinformatics 17:82

Dellicour S, Rose R, Faria NR, Lemey P, Pybus OG (2016) SERAPHIM: studying environmental rasters and phylogenetically-informed movements. Bioinformatics 32:3204–6

Authors: Simon Dellicour & Oliver Pybus

Software packages, manual and tutorial are now available from GitHub here.


Seraphim = Studying Environmental Rasters And PHylogenetically Informed Movements

An R package that combines GIS and phylogeographic methods to test whether environmental factors can explain ecological dispersal.

The package can be used to (i) extract the spatio-temporal information contained in spatiotemporally-referenced phylogenies, such as those generated by the phylogeographics method implemented in BEAST, (ii) estimate several spatial epidemiological statistics from these trees, (iii) compute environmental "weights" associated with each phylogenetic branch for one or more specified environmental rasters, (iv) estimate the correlation between the branch duration and the weights associated with each branch, and (v) test the statistical significance of these correlations using null models.

Seraphim is released under a GNU Lesser General Public License.