eDNAmap: instruction
16 Oct. 2026
Overview

eDNAmap is software that analyzes species/ASV tables obtained from environmental DNA metabarcoding analysis to compare species distribution and biota. The database consists of species/ASV lists obtained from regions centered around the western North Pacific Ocean.
Users can,

1. investigate the distribution of species you're interested in.
2. upload a species/ASV list with individual counts/sequence numbers and compare species composition between sampling locations.
3. plot sampling locations on a map.


Tutorial
As an example, we will upload and analyze the OUT_Miya22.xlsx file (Miya et al. 2022) obtained from the coastal waters of the Boso Peninsula.
The user uploads the OUT_Miya22.xlsx file, which consists of the Reads sheet and Location sheet (see below), from the "Species/ASV table > Upload excel file" option and then presses the SUBMIT button.

Search species:
(1) Search for the species name selected from the dropdown menu.
(2) Search for the keyword entered in the text box.
(3) Search by uploading a list of species names or ASV-IDs.
If an upload file is present (3), the search words from steps (1) and (2) will not be used.
Station name on map: Specify whether to plot the station names on the map.
ASV comparison criteria: Restrict the use of ASVs with few detection points when comparing species/ASV compositions among points for nMDS and cluster analysis.
Distance method for composition comparison: Specify whether to use the Jaccard or Bray-Curtis method as the distance measure when performing comparative analysis of species/ASV compositions among stations. For the Bray-Curtis method, the numbers in the ASV file must be written as percentages.
PDF file: You can choose whether to output the analysis results as PDF files.
Species/ASV table: Select already installed species/ASV tables for analysis. You can also compare them with the species/ASV table uploaded by the user.
 
Input file: Enter the read and location information into the .xlsx file.
 
Outputs: Click the link next to "Status > Finished" to download. Analysis results on the viento and os3 servers are retained for 30 days. Please download any results you need within this period.

Users can independently perform PERMANOVA and environmental correlation analyses using various .R scripts downloaded as outputs.
 
Fish Habitat Lookup

Fish Habitat Lookup checks freshwater, brackish-water, and marine habitat records for a list of scientific names using FishBase data, with synonym matching and Japanese names where available. Created September 19, 2026.
 
History
16 Oct 2026 v1.0.4:
  • Added "Species detection around Japan": instant maps for 1,975 taxa from 19 projects, with PNG/vector PDF downloads.
  • Grouped dropdowns by family; labeled candidate, unidentified, and freshwater taxa; added Japanese names.
  • Reduced map markers and corrected 13 habitat records.
6 Sep 2026 v1.0.3: Security improvements were added for file uploads,
input validation, session keys, error handling, and uploaded filenames.
2 Mar 2026
v1.0.2: Cartopy was added alongside the Generic Mapping Tools (GMT).
4 Feb 2026 New option added: Mode (Mapping or Copmaring-species-lists).
4 Feb 2026 New ASV/OTU table added: KS20-13, S21-3,S21-8,S21-11,S21-12,S21-24,H22-1,H22-3,H22-4,S22-7,S22-11,S22-15,S23-2,H23-2
 
Dependencies
Table handling: pandas
Map tools: Cartopy
Haetmap: pheatmap in R, Version 4.3.2.
nMDS, PERMANOVA, hclust: vegan in R
 
Citation

Inoue J, Hirai J, Ikeba K, Yu Z, Ahmed SI, Lin Z, Lin Y, Wong MK-S, Shinzato C, Itoh S, Ito S-i, Saito H, Hyodo S. 2026. eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish. Molecular Ecology Resources 26:e70066. Link.