Other software – University of Copenhagen

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Other software

WorldMap (Paul Williams)


Biologists needing to estimate richness in a particularly valued currency of different genes or characters are usually unable to measure this directly, or at best are only able to study small samples of genes or characters. However, because genes and characters are inherited, biologists have been able to respond by proposing phylogenetic or taxonomic measures of diversity. These measures predict the biodiversity value of different biotas, using knowledge of the genealogical (or hierarchical) relationships among organisms in combination with models of gene or character evolution

EcoSim (Nicholas Gotelli, Gary Entsminger)

EcoSim is an interactive computer program for null model analysis of many aspects of community ecology, including patterns of species co-occurrence, species diversity, niche and size overlap as well as patterns in macroecology. EcoSim performs Monte Carlo randomizations to create “pseudo-communities”, then statistically compares the patterns in these randomized communities with those in the real data matrix. The program is accompanied by a help file, a tutorial and sample data sets.

EstimateS (Rob Colwell)

An essential tool for analysing diversity on the level of the local community, EstimateS 7 is a free software application for Windows and Macintosh operating systems that computes a variety of biodiversity functions, estimators, and indexes. Included are a wide range of species richness estimators for abundance and incidence (presence/absence) data (Chao, Jackknife, ICE, ACE and others). It also contains diversity indices (Shannon, Simpson, Fisher's alpha) as well as similarity indices (Jaccard, Sørensen, Bray-Curtis, and Morista-Horn).

SAM (Thiago Rangel)

SAM (Spatial Analysis in Macroecology) is a package of statistical tools for spatial analysis, mainly for applications in Macroecology and Biogeography. SAM runs under Microsoft Windows as as a menu-driven, graphical interface computational program. SAM offers a wide spectrum of statistical methods currently used in Surface Pattern Spatial Analysis. Among the tools are Trend Surface Analysis, PCNM or Eigen-based Spatial Filtering, Spatial Generalised Least Squares, and Simultaneous or Conditional Autoregrssive Models.

Software that evaluates the Mid-domain effect

RangeModel (Rob Colwell)

RangeModel is a randomisation tool for analysing one-dimensional patterns in species richness. It specifically analyses patterns known as the Mid-domain effect (MDE) by randomising empirical or theoretical species ranges. Simulations can be compared with empirical patterns, and simulated distributions and richness patterns, as well as confidence intervals, can be exported. It is freely downloadable and there is an online users guide on the site.

Mid-domain Null (Christy McCain)

This is a randomisation model similar to RangeModel. It allows for sampling of ranges for randomisation with or without replacement and has other additional features, described in a 2004 paper (Journal of Biogeography 31: 19-31). The model is available upon request from the author, Christy McCain.

GEOSPOD (Walter Jetz)

This is a Monte Carlo simulation program to model the effect of geometric constraints and area on large-scale patterns in species richness. GEOSPOD calculates both 1-dimensional and 2-dimensional patterns, but sofar 2-dimensional templates are available only for simple circle or quadratic shapes as well as for Subsaharan Africa.

GIS Software and Data


The main provider of GIS software provides an extensive array of guidelines and tools online. This system is the main GIS at CMEC.


http://www.qgis.org/en/site/a cross-platform free and open-source desktop GIS application that provides data viewing, editing, and analysis capabilities.

Geospatial Modelling Environment


GME provides you with a suite of analysis and modelling tools, ranging from small 'building blocks' that you can use to construct a sophisticated work-flow, to completely self-contained analysis programs: 


A videspread rasterbased GIS. Geospatial software for monitoring and modeling the Earth system. Delivered by the non-profit research institute Clark Labs. CMEC has a minor number of licenses.  http://clarklabs.org/ 


The Information and Service System for European Coordinate Reference Systems (CRS) provides guidance in solving problems with e.g. projections and transformation.
The European Environment Information and Observation Network (EIONET) contains links to guidelines, templates and services for use when handling spatial data, maps and geographical information systems.

Data and Maps

EEA Dataservice and maps


The dataservice of the European Environmental Agency provides almost all data sets and applications which have been used in EEA's periodical environmental reports.

ESDI (Earth Science Data Interface)
The Earth Science Data Interface is the data-providing portal of The Global Land Cover Facility. GLFC is a research program under NASA, hosted by University of Maryland. Here you can find some of the most comprehensive global datasets, including the MODIS vegetation cover maps, GIS layers of IUCN protected areas, as well as the AVHRR global land cover and primary production maps.
The GEO data portal of The United Nations Environment Programme. It holds many geospatial maps, covering themes like Freshwater, Population, Forests, Emissions, Climate, Disasters, Health and GDP. These are however not available in GIS-format.
ArcGIS Resources
Read: http://resources.arcgis.com
or read about ArcGIS Online:  
ICES (I`nterbational Council for Exploration of the Sea) is the organisation that coordinates and promotes marine research in the North Atlantic. Their portal contains many oceanographic and realted datasets.
United States Geological Survey (USGS) is the extensive source for all kinds of GIS maps covering the USA.
The Land Processes Distributed Active Archive Center (LPDAAC) disseminates global land processes data, collected by various satellite and aerial sensors. Datasets available here include Terra ASTER, MODIS vegetation cover, Landsat Pathfinder, the Global 30 Arc-Second Elevation Data Set and others.
Landuse maps (Denmark)

http://www.dmu.dk (Older Danish landuse maps) and landuse maps from 2012: Basemap

(Other GIS datasets available at:

EEA Global Landcover: http://www.eea.europa.eu

Oak Ridge National Laboratory, Geographic Information Science and Technology: http://www.ornl.gov/sci/gist)