Community phylogenetics (or eco-phylogenetics) combines ecology and evolutionary biology, linking ecological phenomena with the evolutionary processes that generate species and their traits (see Webb et al., 2002). Source text: Pearse et al., 2015.
It is committed to heightening awareness about the diversity of life on earth, its evolutionary history and the threats of extinction. OneZoom allows you to explore the tree of life in a completely new way: it's like a map, everything is on one page, all you have to do is zoom in and out. OneZoom also provides free, open source, data visualisation tools for science and education, currently focusing on the tree of life.
An integrated development environment for ecological modelling. Bio7 contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
A package for the R software dedicated to the analysis of comparative evolutionary data. Adephylo provides tools for quantifying and describing the phylogenetic structures of biological traits. adephylo implements tests of phylogenetic signal, phylogenetic distances and proximities, and novel methods for describing further univariate and multivariate phylogenetic structures.
A cross-platform package, written for the R environment, for studying partitioning of diversity among natural communities in space and time. Complementing and extending existing software, spacodiR allows for hypothesis testing and parameter estimation in studying spatial structuring of species-, phylogenetic- and trait diversities.
Allows measurement, modelling and simulation of phylogenetic structure in environmental data. pez contains the first implementation of methods, and compiles existing data structures and methods into a single, coherent package. It simplifies the calculation and comparison more than 30 metrics, grouped into four categories: shape, evenness, dispersion, and dissimilarity.
Provides knowledge towards understanding the roles of microbes in the underlying disease mechanism. miLineage develops a general framework to: (a) perform robust association tests for the microbial community that exhibits arbitrary inter-taxa dependencies; (b) localize lineages on the taxonomic tree that are associated with covariates (e.g. disease status); (c) assess the overall association of the whole microbial community with the covariates. Unlike existing methods for microbiome association analysis, this framework does not make any distributional assumptions on the microbiome data; it allows for the adjustment of confounding variables and accommodates excessive zero observations and it incorporates taxonomic information.
An easy way for ecologists to make realistic, tenable phylogenies. With phyloGenerator, you can download real DNA sequence data for your species of interest, and then generate a calibrated phylogeny using a defensible constraint tree. Your phylogeny may not be 'correct', but it will have branch lengths based on DNA data and its topology will be safe. It'll be a 'real' phylogeny, not a best-guess from taxonomy filled with polytomies. You don't need to have an advanced knowledge of phylogenetics to use phyloGenerator. Just download the program, follow the guide, and you can build a phylogeny in minutes.
A web-based application that integrates biodiversity information aggregated from many sources with phylogenetic trees. PhyloJIVE demonstrates that it is possible and useful to assemble interactive biodiversity data from diverse sources. Viewed through phylogeny, the evolutionary context of morphological, spatial and ecological data becomes clear and accessible to non-specialists.
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