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)http://homepages.together.net/~gentsmin/ecosim.htm
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)http://viceroy.eeb.uconn.edu/EstimateS
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)http://www.ecoevol.ufg.br/sam
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)http://viceroy.eeb.uconn.edu/RangeModel
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)http://www.nceas.ucsb.edu/~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)http://evolve.zoo.ox.ac.uk/software.html?id=geospod
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.