Biodiverse

A tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic, trait and matrix-based relationships, as well as related environmental and temporal variations.
https://github.com/shawnlaffan/biodiverse

Category: Biosphere
Sub Category: Biodiversity Analysis and Metrics

Keywords

beta-diversity biodiverse endemism hacktoberfest phylodiversity phylogenetic-diversity phylogenetic-trees phylogeography randomisations spatial-analysis species-turnover

Last synced: about 20 hours ago
JSON representation

Repository metadata

A tool for the spatial analysis of diversity

Host: GitHub
URL: https://github.com/shawnlaffan/biodiverse
Owner: shawnlaffan
License: gpl-3.0
Created: 2015-03-27T22:49:20.000Z (over 11 years ago)
Default Branch: master
Last Pushed: 2026-10-29T00:36:04.000Z (about 22 hours ago)
Last Synced: 2026-10-29T03:01:41.576Z (about 20 hours ago)
Topics: beta-diversity, biodiverse, endemism, hacktoberfest, phylodiversity, phylogenetic-diversity, phylogenetic-trees, phylogeography, randomisations, spatial-analysis, species-turnover
Language: Perl
Homepage: http://shawnlaffan.github.io/biodiverse/
Size: 457 MB
Stars: 82
Watchers: 7
Forks: 19
Open Issues: 62
Releases: 27
Metadata Files:
- Readme: README.md
- License: LICENSE

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.

DOWNLOAD: Biodiverse can be downloaded from https://github.com/shawnlaffan/biodiverse/wiki/Downloads

Biodiverse supports the following processes:

Linked visualisation of data distributions in geographic, taxonomic, phylogenetic and matrix spaces;
Spatial moving window analyses including richness, endemism, phylogenetic diversity and beta diversity;
Spatially constrained agglomerative cluster analyses;
Spatially constrained region grower analyses;
Interactive visualisation of turnover patterns (for example beta-diversity); and
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 300 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 https://groups.google.com.au/group/biodiverse-users and a blog at https://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 1.0".

Laffan, S.W., Lubarsky, E. & Rosauer, D.F. (2010) Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography. Vol 33, 643-647 (Version 1.0).

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

Installation

Installation instructions can be accessed through the Installation page.

News

See https://shawnlaffan.github.io/biodiverse/#news

Acknowledgements

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

Much of the original GUI coding was by Eugene Lubarsky. Substantial contributions to the project have also been made by Michael Zhou and Anthony Knittel. Unfortunately the code history does not show their contributions as authorship details were lost as we transitioned from Google Code to GitHub.

Persistent URL

https://www.purl.org/biodiverse

Keywords

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

Owner metadata

Name:
Login: shawnlaffan
Email:
Kind: user
Description:
Website: http://shawnlaffan.github.io/biodiverse/
Location: Australia
Twitter:
Company: @unsw-edu-au
Icon url: https://avatars.githubusercontent.com/u/1332405?u=2335aca63418740989c7eb5001cdf88f94aec53d&v=4
Repositories: 73
Last ynced at: 2026-10-25T01:22:14.612Z
Profile URL: https://github.com/shawnlaffan

GitHub Events

Total

Create event: 94
Delete event: 96
Discussion event: 1
Gollum event: 37
Issue comment event: 22
Issues event: 35
Pull request event: 118
Push event: 259
Release event: 2
Watch event: 4

Last Year

Create event: 58
Delete event: 68
Discussion event: 1
Gollum event: 7
Issue comment event: 2
Issues event: 9
Pull request event: 55
Push event: 121
Release event: 1
Watch event: 1

Committers metadata

Last synced: 3 days ago

Total Commits: 5,932
Total Committers: 15
Avg Commits per committer: 395.467
Development Distribution Score (DDS): 0.07

Commits in past year: 906
Committers in past year: 2
Avg Commits per committer in past year: 453.0
Development Distribution Score (DDS) in past year: 0.007

Name	Email	Commits
Shawn Laffan	s**n@g**m	5514
Luke Fitzpatrick	l**k@g**m	202
zhoumichaely@gmail.com	z**y@gm@0**0	81
Dan Rosauer	D****r	41
Anderson Ku	a**u@g**m	40
Jason Mumbulla	j**a@g**m	37
dependabot[bot]	4****]	6
anthony.knittel@gmail.com	a**l@gm@0**0	3
Katherine Spice	k**e@c**k	2
Patrice Clement	m**p@g**g	1
Liuyong Ding	3****s	1
Katrin Leinweber	9****r	1
Alex Kapranoff	a**x@k**u	1
sjb01230@gmail.com	s**0@gm@0**0	1
Anderson Ku	a**u@a**m	1

Committer domains:

Issue and Pull Request metadata

Last synced: 2 days ago

Total issues: 56
Total pull requests: 186
Average time to close issues: almost 2 years
Average time to close pull requests: about 16 hours
Total issue authors: 8
Total pull request authors: 3
Average comments per issue: 1.07
Average comments per pull request: 0.03
Merged pull request: 171
Bot issues: 0
Bot pull requests: 2

Past year issues: 6
Past year pull requests: 63
Past year average time to close issues: 22 days
Past year average time to close pull requests: about 2 hours
Past year issue authors: 1
Past year pull request authors: 2
Past year average comments per issue: 0.17
Past year average comments per pull request: 0.0
Past year merged pull request: 60
Past year bot issues: 0
Past year bot pull requests: 2

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/shawnlaffan/biodiverse

Top Issue Authors

shawnlaffan (46)
GoogleCodeExporter (4)
eortizb (1)
sonqollay (1)
vmikk (1)
luishdez35 (1)
FranckLejzerowicz (1)
hlstrived (1)

Top Pull Request Authors

shawnlaffan (183)
dependabot[bot] (2)
vmikk (1)

Top Issue Labels

GUI (25)
enhancement (16)
bug (6)
needs blog post (5)
randomisations (5)
trees (4)
auto-migrated (4)
Gtk3 (3)
Priority-Medium (2)
closable? (2)
spatial conditions (2)
Type-Defect (1)
indices (1)
executable (1)
OpSys-OSX (1)
data import (1)
locale (1)
Type-Enhancement (1)
tests (1)

Top Pull Request Labels

github_actions (2)
dependencies (2)

Package metadata

Total packages: 3
Total downloads: unknown
Total dependent packages: 1 (may contain duplicates)
Total dependent repositories: 0 (may contain duplicates)
Total versions: 36
Total maintainers: 1

proxy.golang.org: github.com/shawnlaffan/biodiverse

Homepage:
Status: removed
Documentation: https://pkg.go.dev/github.com/shawnlaffan/biodiverse#section-documentation
Licenses: gpl-3.0
Latest release: v0.0.0-20260904233553-349eed75a8c0 (published about 2 months ago)
Last Synced: 2026-10-28T02:36:30.283Z (2 days ago)
Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Rankings:
- Dependent packages count: 4.373%
- Average: 4.52%
- Dependent repos count: 4.668%

metacpan.org: Task-Biodiverse-NoGUI

Task for Biodiverse dependencies for non-GUI use [DEPRECATED]

Homepage:
Licenses: unknown
Latest release: 3.2 (published almost 4 years ago)
Last Synced: 2026-10-28T02:36:29.991Z (2 days ago)
Versions: 26
Dependent Packages: 1
Dependent Repositories: 0
Rankings:
- Dependent repos count: 1.554%
- Average: 9.726%
- Dependent packages count: 17.898%
Maintainers (1)
- SLAFFAN

metacpan.org: Task-Biodiverse

Task for Biodiverse dependencies [DEPRECATED]

Homepage:
Licenses: unknown
Latest release: 3.2 (published almost 4 years ago)
Last Synced: 2026-10-28T02:36:29.862Z (2 days ago)
Versions: 9
Dependent Packages: 0
Dependent Repositories: 0
Rankings:
- Dependent repos count: 1.554%
- Average: 16.881%
- Dependent packages count: 32.208%
Maintainers (1)
- SLAFFAN

Dependencies

.github/workflows/linux_de_locale.yml actions

actions/cache v3 composite
actions/checkout v3 composite
shogo82148/actions-setup-perl v1 composite

.github/workflows/macos.yml actions

actions/cache v3 composite
actions/checkout v3 composite

.github/workflows/windows.yml actions

actions/cache v3 composite
actions/checkout v3 composite

Makefile.PL cpan

META.json cpan

Alien::Build::Plugin::Fetch::Cache 0
Class::Inspector 0
Clone 0.35
Cpanel::JSON::XS 3
Data::Compare 0
Data::Section::Simple 0
Data::Structure::Util 0
Devel::Symdump 0
Excel::ValueReader::XLSX 0
Exception::Class 0
Exporter::Easy 0
File::BOM 0
File::Compare 0
File::Find::Rule 0
Geo::Converter::dms2dd 0.05
Geo::GDAL::FFI 0.09
Geo::ShapeFile 3.00
Getopt::Long::Descriptive 0
HTML::QuickTable 0
JSON::MaybeXS 1.003
JSON::PP 0
List::MoreUtils 0.425
List::Unique::DeterministicOrder 0.003
List::Util 1.54
Math::Polygon 0
Math::Random::MT::Auto 6.21
Perl::Tidy 0
Readonly 0
Ref::Util 0
Ref::Util::XS 0
Regexp::Common 0
Scalar::Util::Numeric 0
Sereal 3
Sort::Key 0
Spreadsheet::ParseExcel 0
Spreadsheet::ParseODS 0
Spreadsheet::ParseXLSX 0
Spreadsheet::Read 0.82
Spreadsheet::ReadSXC 0.28
Statistics::Descriptive 3.0608
Statistics::Descriptive::PDL 0.15
Statistics::Sampler::Multinomial 1.02
Test2::Suite 0
Test::Deep::NoTest 0
Test::Lib 0
Test::TempDir::Tiny 0
Text::CSV_XS 1.52
Text::Fuzzy 0
Text::Wrapper 0
Tree::R 0
URI::Escape 0
URI::Escape::XS 0
YAML::Syck 1.29
autovivification 0.18
parent 0
perl 5.036
rlib 0

etc/bundles/GUI/Makefile.PL cpan

ExtUtils::Depends * build
ExtUtils::PkgConfig * build
Glib * build
Gtk3 * build
Pango * build
Browser::Start *
Data::DumpXML *
Gnome2::Canvas *
HTTP::Tiny *
IO::Socket::SSL *
LWP::Simple *
Task::Biodiverse::NoGUI 3.000
Test2::V0 * test

etc/bundles/NoGUI/Makefile.PL cpan

Data::Section::Simple * build
Devel::Symdump * build
File::Compare * build
Perl::Tidy * build
Scalar::Util::Numeric * build
Test2::V0 * build
Class::Inspector *
Clone 0.35
Cpanel::JSON::XS 3
DBD::XBase *
Data::Alias *
Data::Compare *
Data::DumpXML *
Data::Structure::Util *
Exception::Class *
Exporter::Easy *
File::BOM *
Geo::Converter::dms2dd 0.05
Geo::GDAL::FFI 0.07
Geo::ShapeFile 3.00
Geo::Shapefile::Writer *
Getopt::Long::Descriptive *
HTML::QuickTable *
JSON::MaybeXS 1.003
JSON::PP *
List::BinarySearch 0.25
List::BinarySearch::XS 0.09
List::MoreUtils 0.425
List::Unique::DeterministicOrder *
List::Util 1.45
Math::Polygon *
Math::Random::MT::Auto 6.21
Path::Class *
PkgConfig 0.21026
Readonly *
Ref::Util 0.101
Regexp::Common *
Sereal 3
Sort::Key::Natural *
Sort::Naturally *
Spreadsheet::ParseExcel *
Spreadsheet::ParseXLSX *
Spreadsheet::Read 0.60
Spreadsheet::ReadSXC *
Statistics::Descriptive 3.0608
Statistics::Sampler::Multinomial *
Test2::V0 0.000130
Test::TempDir::Tiny 0.016
Text::CSV_XS 1.04
Text::Fuzzy *
Text::Levenshtein *
Text::Wrapper *
Tree::R *
URI::Escape::XS *
YAML::Syck 1.29
autovivification 0.16
parent *
rlib *

cpanfile cpan

Alien::Build::Plugin::Fetch::Cache *
Browser::Start *
Class::Inspector *
Clone 0.35
Cpanel::JSON::XS 3
Data::Compare *
Data::DumpXML *
Data::Section::Simple *
Data::Structure::Util *
Devel::Symdump *
Excel::ValueReader::XLSX *
Exception::Class *
Exporter::Easy *
ExtUtils::Depends *
ExtUtils::PkgConfig *
FFI::Platypus::Declare *
Faster::Maths *
File::BOM *
File::Compare *
File::Find::Rule *
Geo::Converter::dms2dd 0.05
Geo::GDAL::FFI 0.15
Geo::ShapeFile 3.00
Getopt::Long::Descriptive *
Glib *
Gtk3 *
HTML::QuickTable *
HTTP::Tiny *
Hash::Util::Set *
Hash::Util::Set::XS *
IO::Socket::SSL *
JSON::MaybeXS 1.003
JSON::PP *
LWP::Simple *
List::MoreUtils 0.425
List::Unique::DeterministicOrder 0.003
List::Util 1.54
Math::AnyNum *
Math::Polygon *
Math::Random::MT::Auto 6.21
PDL::GSL::CDF *
PPR *
Pango *
Readonly *
Ref::Util *
Ref::Util::XS *
Regexp::Common *
Scalar::Util::Numeric *
Sereal 3
Sort::Key *
Spreadsheet::ParseExcel *
Spreadsheet::ParseODS *
Spreadsheet::ParseXLSX *
Spreadsheet::Read 0.82
Spreadsheet::ReadSXC 0.28
Statistics::Descriptive 3.0608
Statistics::Descriptive::PDL 0.15
Statistics::Sampler::Multinomial 1.02
Test2::Suite *
Test::Deep *
Test::Deep::NoTest *
Test::Exception *
Test::Lib *
Test::Most *
Test::TempDir::Tiny *
Text::CSV_XS 1.52
Text::Fuzzy *
Text::Wrapper *
Tree::R *
Tree::STR 0.06
URI::Escape *
URI::Escape::XS *
Win32::LongPath *
YAML::Syck 1.29
autovivification 0.18
parent *
rlib *
Data::Recursive * suggests
Panda::Lib * suggests
Test2::Harness * suggests

Score: 8.364042011922063

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Sustainable Technology

Biodiverse

Keywords

Repository metadata

README.md

Biodiverse

Installation

News

Acknowledgements

Persistent URL

Keywords

Owner metadata

GitHub Events

Total

Last Year

Committers metadata

Committer domains:

Issue and Pull Request metadata

Top Issue Authors

Top Pull Request Authors

Top Issue Labels

Top Pull Request Labels

Package metadata

proxy.golang.org: github.com/shawnlaffan/biodiverse

metacpan.org: Task-Biodiverse-NoGUI

metacpan.org: Task-Biodiverse

Dependencies