Phylojive – Integrating Biodiversity data with the Tree of Life

Phylojive

:: DESCRIPTION

PhyloJive (Phylogeny Javascript Information Visualiser and Explorer) is a web based application that places biodiversity information aggregated from many sources onto compact phylogenetic trees.

::DEVELOPER

Joe Miller

:: SCREENSHOTS

:: REQUIREMENTS

Web Browser
JS

:: DOWNLOAD

Phylojive

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1308-9. doi: 10.1093/bioinformatics/btu024. Epub 2014 Jan 17.
PhyloJIVE: Integrating biodiversity data with the Tree of Life.
Jolley-Rogers G1, Varghese T, Harvey P, dos Remedios N, Miller JT.

BIDDSAT 0.3 – BIoDiversity DataSet Assessment Tool

BIDDSAT 0.3

:: DESCRIPTION

BIDDSAT is an online tool that enables selected diagnostic visualizations on the content of data publishers and/or their individual collections.

::DEVELOPER

Javier Otegui

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser
PHP

:: DOWNLOAD

BIDDSAT

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2207-8. doi: 10.1093/bioinformatics/bts359. Epub 2012 Jun 23.
BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network.
Otegui J, Ariño AH.

bdvis 0.2.28 – Biodiversity Data Visualizations

bdvis 0.2.28

:: DESCRIPTION

bdvis provides a set of functions to create basic visualizations to quickly preview different aspects of biodiversity information such as inventory completeness, extent of coverage (taxonomic, temporal and geographic), gaps and biases.

::DEVELOPER

Vijay Barve

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX / Windows
R

:: DOWNLOAD

bdvis

:: MORE INFORMATION

Citation

bdvis: visualizing biodiversity data in R.
Barve V, Otegui J.
Bioinformatics. 2016 Jun 10. pii: btw333.

CANGS 1.1 – Process & Anylyze 454 GS-FLX data in Biodiversity studies

CANGS 1.1

:: DESCRIPTION

CANGS (Cleaning and Analyzing Next Generation Sequences) is a utility, which is designed to automate the process of trimming sequences, filtering low quality sequences and performing various analyses for diversity study. There are basically two layers in CANGS 1) processing layer and 2) Analysis Layer.

::DEVELOPER

Institute of Population Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Perl
Bioperl
Blast
MAFFT

:: DOWNLOAD

CANGS

:: MORE INFORMATION

Citation:

CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.
Pandey RV, Nolte V, Schlštterer C.
BMC Res Notes. 2010 Jan 11;3:3.

Biota 3.00 – Biodiversity Database Manager

Biota 3.00

:: DESCRIPTION

Biota manages specimen-based, spatially and taxonomically referenced data for ecologists, conservation biologists, evolutionary biologists, systematists, museums and herbaria.

::DEVELOPER

Robert K. Colwell

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX

:: DOWNLOAD

Biota

:: MORE INFORMATION

Citation

Colwell, R. K. 2004.
Biota 2: The biodiversity database manager.
Sinauer Associates, Sunderland, MA.