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.
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.
Furnishes a methodology for managing correlated outcome data in microbiome association studies. SSKAT implements small-sample adjusted kernel machine association tests for different actions: multivariate continuous outcome (mSKAT); univariate continuous and binary outcome (aSKAT); and correlated continuous outcome (cSKAT). Furthermore, cSKAT can be employed for testing associations between microbiome compositions and an outcome of interest.
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 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.
Permits to annotate genome function of Atlantic salmon, considering species and populations of major scientific interest. FAASG exploits unique features of salmonid biology, including recent whole genome duplication (WGD) and extensive phenotypic variation at both macro- and micro-evolutionary timescales. It can generate broad mechanistic insights into genome evolution and adaptation. The platform aims to report progress, including experimental and computational protocols, publications and datasets, along with contact information for interested researchers.
Provides a phylogenetic view of biodiversity data. PhyloJIVE is a web-based application that integrates biodiversity information aggregated from many sources. It demonstrates how to navigate the tree and component clades, to adjust the visualization and other parameters. It can also select taxon character states, fetch character sets from Identify Life and display the results of web service queries on the tree.