DNA-based Taxonomic Relatedness
This workflow assesses the taxonomic relationships among taxa in pelagic samples. It provides insight into community structure and the underlying ecological processes. First, species-level assignments from PEMA are harmonised against a standard taxonomy, such as WoRMS. Then, pairwise taxonomic distances are calculated using the Remote Virtual Laboratory for Taxonomic Computing (RvLab; Varsos et al. 2016), producing a distance matrix that captures distance among all detected species (taxa). This matrix can be normalised as needed and serves as the basis for diversity metrics, such as Faith's phylogenetic diversity, mean pairwise distance (MPD), or mean nearest taxon distance (MNTD). When relative abundance data are available, they can be incorporated to weight individual taxa. The resulting numerical index helps track shifts in community composition, detect homogenisation, and identify losses in taxonomic and functional diversity.
Default
- Date ( Publication)
- 2025-10-01
- Status
- Completed
- Version
-
1.0.0
- Keywords
-
relatedness
- Keywords
-
taxonomy
- Keywords
-
DNA-based
- Keywords
-
metabarcoding
- Keywords
-
pelagic habitats
- Keywords
-
PEMA
- Keywords
-
WoRMS
- Keywords
-
RvLab
- Access constraints
- License
- Use limitation
-
GPLv3 - <a href=" https://www.gnu.org/licenses/gpl-3.0.html" target="_blank"> https://www.gnu.org/licenses/gpl-3.0.html</a>
- OnLine resource
-
Link to the workflow
(
WWW:LINK-1.0-http--link
)
- Service Name
-
PEMA Runner
- Service Description
-
This service aims at running PEMA on all the sequences passed as input. It also requires a parameter file (a tsv file).
- Service Reference (id)
- Service Name
-
PEMA Converter
- Service Description
-
This service aims to reformat and produce final output in various formats for human and machine2machine reading.
- Service Reference (id)
- Service Name
-
PEMA Sequences Retriever
- Service Description
-
This service aims to download the sequences files (fasq files) in order to run PEMA.
- Service Reference (id)
- Service Name
-
ARMS OTU Unifier
- Service Description
-
This service aims at creating an OTU table with species information that can be processed by WoRMS and WRIMS.
- Service Reference (id)
- Service Name
-
ARMS WoRMS Taxonomic Checker
- Service Description
-
WoRMS taxon match webservice to check for the WoRMS match.
- Service Reference (id)
- Service Name
-
ARMS WRiMS Invasive Checker
- Service Description
-
WRIMS taxon match webservice to check the known distribution of the species.
- Service Reference (id)
- Service Name
-
Taxa2Dis
- Service Description
-
This service aims at transforming the matrix of the WRiMS component output into a valid format (agg_matrix) for the taxa2dis function.
- Service Reference (id)
- Service Name
-
Taxon Dive
- Service Description
-
This service aims at calculating taxonomic distinction metrics per sample (Δ+, expectation, and dispersion), export the results, and generate a graph with the results.
- Service Reference (id)
- Workflow Helpdesk
metadataMetadata
- File identifier
- 39780f54-1297-48ed-a9e3-2eb4e6e363ba XML
- Metadata language
- en
- Hierarchy level
- Workflow
- Metadata Schema Version
-
1.0
