SOFTWARE

Further on-going projects can be found on the Antonelli lab GitHub page.

Sampbias [Link]

Sampbias is a method and tool to 1) visualize the distribution of occurrence records and species in any user-provided dataset, 2) quantify the biasing effect of geographic features related to human accessibility, such as proximity to cities, rivers or roads, and 3) create publication-level graphs of these biasing effects in space.

SpeciesGeoCoder [Link]

We have developed a software for coding species into user-defined units for e.g. biogeographic analyses, using a combination of GIS polygons and altitudinal ranges. There are two main packages: one written in python and another in R. The python program available via the link above is described in a pre-print A simplified Graphical User Interface (GUI) available from sourceforge; see more details on the package's wiki page. The R package is available from CRAN.

Infomap Bioregions [Link]

Daril Vilhena and Alexandre Antonelli recently described a network method for delimiting biogeographical regions based on species occurrence data (Vilhena and Antonelli 2015, Nature Communications). We have since then made this method available for public use in Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps. Species distributions may be provided as georeferenced point occurrences or range maps, and can be of local, regional or global scale. The application uses a novel adaptive resolution method to make best use of often incomplete species distribution data. The application is fully described here.

PyRate [Link]

PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. Different Bayesian algorithms are available to assess the presence of temporal rate shifts by exploring alternative diversification models. The methods and program are described here and here.

SUPERSMART [Link]

SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages and Relationships of Taxa) is a platform for automated mining of molecular sequences, large-scale phylogenetic inference and fossil calibration. The methods are described here.