Plankton Toolbox The Plankton Toolbox is a free tool for aquatic scientists, and others, working with environmental monitoring related to phyto- and zooplankton. Features include: Import phyto- or zooplankton data in .txt and .xlsx files in different formats (configurable) Work with data on abundance, biovolume and carbon content Data screening - quality control of data Aggregate data, e.g. from species level to class level Plotting tools Statistics (in early development) Export data in .txt or .xlsx for further analyses or plotting A future update with functionality for using Plankton Toolbox as a counting tool by the microscope is planned. Developed by: Nordic Microalgae is developed and operated by the Swedish Meterological and Hydrological Institute (SMHI http://www.smhi.se/en) with funding from the Swedish LifeWatch project http://svenskalifewatch.se/. Technology or platform: The software is available as version 1.0.0 for Windows and MacOS. Version 1.0.1 is available for Windows. A Linux version will be produced upon request.

The AZTI Marine Biotic Indix (AMBI) is software developed by AZTI-Tecnalia for assessing the quality of benthic macro-invertebrates assemblages by calculating the homonymous index. It was developed in order to establish the ecological quality of European coasts and estuaries. This tool explores the response of soft-bottom communities to natural and man-induced changes in water quality, integrating long-term environmental conditions. The software includes near 8.000 taxa from all seas, representative of the most important soft-bottom communities present at estuarine and coastal systems, from the North Sea to the Mediterranean, North and South America, Asia, etc. This tool allows you to easily calculate the AMBI, represent your data and export results. You must use the guidelines published in Marine Pollution Bulletin. Version 5.0, from May 2012, allows importing more than 255 samples from an Excel file, with the updated species list from November 2014. Developed by: The AZTI Marine Biotic Index (AMBI) is developed by AZTI-Tecnalia. Used in tools: Since February 2012, the Steering Committee of the Salmon Aquaculture Dialogue, promoted by WWF (World Wildlife Fund), has included the toll AMBI as one of the indicators to assess the environmental impact of farmed salmon, worldwide. Technology or platform: AMBI is a software for WXP, W7 and W8.

IMNGS is a platform that uniformly and systematically screens for, retrieves, processes, and analyses all available prokaryotic 16S rRNA gene amplicon datasets from public repositories and uses them to build sample-specific sequence databases and OTU-based profiles. The retrieved information can be used to address questions of relevance in microbial ecology, for example with respect to the occurrence of specific microorganisms in different ecosystems or to perform targeted diversity studies. IMNGS also offers a complete pipeline for de novo analysis of a user's own raw amplicon sequencing data generated using the Illumina technology. Due to the personalised nature of many functions and the high computational cost related to the performed tasks, only registered users can submit jobs (registration can be done via the IMNGS home page; regsiter there as a Guest to learn more about what it can do). The IMNGS web interface can then be used to: search and select datasets/samples (runs), create and launch jobs, and inspect the outputs of the jobs. Developed by: Ilias Lagkouvardos, Technical university of Munich (TUM) Used data resources: SRA repository amplicon studies, user query 16S sequence, user raw amplicon sequences Used in tools: USEARCH Technology or platform: Django, Python, PostgreSQL

Rhea: R scripts for the analysis of microbial profiles The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. The Rhea pipeline is a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalisation steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be used as a framework for advanced users who can modify and expand the tool. Rhea is composed of 6 steps that can be run independently or as a set. Normalization Alpha-Diversity Beta-Diversity Taxonomic-Binning Serial-Group-Comparisons Correlations