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A tool for the spatial analysis of diversity
Perl Other

Indices table now lists both cluster and region grower as grouping op…

…tions. Previously it was only clustering.

Signed-off-by: Shawn Laffan <shawnlaffan@gmail.com>
latest commit e0c8f1b6d8
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README.md

Biodiverse

Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic, trait and matrix-based (e.g. genetic distance) relationships, as well as related environmental and temporal variations. Biodiverse supports the following processes:

  1. Linked visualisation of data distributions in geographic, taxonomic, phylogenetic and matrix spaces;
  2. Spatial moving window analyses including richness, endemism, phylogenetic diversity and beta diversity;
  3. Spatially constrained agglomerative cluster analyses;
  4. Spatially constrained region grower analyses;
  5. Interactive visualisation of turnover patterns (for example beta-diversity); and
  6. Randomisations for hypothesis testing.

Biodiverse is open-source and supports user developed extensions. It can be used both through a graphical user interface (GUI) and through user written scripts.

More than 250 indices are supported. See the Indices page.

Screen shots can be found on the ScreenShots page.

Example applications can be seen at the publications page.

Help can be located via the help pages (these are also accessible via the wiki link on the right of this page).

A discussion group is at http://groups.google.com.au/group/biodiverse-users and a blog at http://biodiverse-analysis-software.blogspot.com.au/

To cite Biodiverse or acknowledge its use, use the following details, substituting the version of the application that you used for "Version 0.17".

An overview of the system is also provided in Dan Rosauer's talk at TDWG2008:

  • Rosauer, D.F. & Laffan, S.W. (2008) Linking phylogenetic trees, taxonomy & geography to map phylogeography using Biodiverse. Taxonomic Data Working Group 2008, Perth, Australia. PPT SWF with audio.

For a list of publications using Biodiverse, see the PublicationsList page.

Installation

Installation instructions can be accessed through the Installation page.

News

27-Oct-2014 A new development release is now available. It can be downloaded from https://purl.org/biodiverse/wiki/Downloads

The summary of changes is at https://purl.org/biodiverse/wiki/ReleaseNotes#version-099_005

27-Oct-2014

A new blog post describing some of the new features in the upcoming 1.0 release is available. http://biodiverse-analysis-software.blogspot.com.au/2014_10_01_archive.html

18-Sep-2014

A new development release is now available. It can be downloaded from https://purl.org/biodiverse/wiki/Downloads

The summary of changes is at https://purl.org/biodiverse/wiki/ReleaseNotes#version-099_004

13-Aug-2014

A Biodiverse pipeline for the CANAPE (Categorical Analysis of Neo and Palaeo Endemism) analyses described in Mishler et al. (2014) is now available. See https://github.com/NunzioKnerr/biodiverse_pipeline

31-Oct-2013

Biodiverse version 0.19 has been released. It can be downloaded from https://bintray.com/shawnlaffan/Biodiverse/Biodiverse-releases .

The summary of changes is at https://purl.org/biodiverse/wiki/ReleaseNotes#version-019

Acknowledgements

This research has been supported by Australian Research Council Linkage Grant LP0562070 (Laffan and West) and UNSW FRGP funding to Laffan.

Persistent URL

http://www.purl.org/biodiverse

Keywords

Biodiversity analysis tool, spatial analysis, phylogeography, spatial analysis, endemism, phylogenetic diversity, beta diversity, species turnover

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