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ABIapp: A user-friendly tool for precise parasitic helminth species delimitation
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  • Abigail Chan,
  • Urusa Thaenkham,
  • Tanaphum Wichaita,
  • Sompob Saralamba
Abigail Chan
Mahidol University Faculty of Tropical Medicine
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Urusa Thaenkham
Mahidol University Faculty of Tropical Medicine
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Tanaphum Wichaita
Mahidol Oxford Tropical Medicine Research Unit
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Sompob Saralamba
Mahidol Oxford Tropical Medicine Research Unit

Corresponding Author:[email protected]

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Abstract

Parasitic helminths are highly diverse and ubiquitously distributed in various environments and hosts. Their vast species diversity makes both morphological and molecular species delimitation challenging. We developed and validated a simple, easy-to-use application, Applying Taxonomic Boundaries for Species Identification (ABIapp), to aid in the delimitation of helminth species. ABIapp utilizes a database of cut-off genetic distances determined by the K-means algorithm to establish helminth taxonomic boundaries for the 18S and 28S rRNA genes, ITS1 and 2 regions, and the 12S and 16S rRNA, COI, COII, cytB, and ND1 genes. ABIapp is written in R, using the Shiny framework to deliver an interactive and user-friendly interface. To assess the accuracy of ABIapp, validation was undertaken both in silico and with actual specimens. In silico validation involved obtaining 591 genetic distances from 117 publications and inputting these into ABIapp, while actual specimen validation was conducted using ten specimens. We also compared the accuracy of ABIapp with other species delimitation servers. We achieved an overall classification accuracy of 76 % and 75 % for in silico and with actual specimens, respectively. Our results underscore the effectiveness and reliability of ABIapp for helminth species delimitation. With its user-friendly interface, minimalistic data input requirements, and robust classification accuracy, ABIapp is a pioneering tool offering helminth researchers an invaluable resource for species delimitation.