iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

Miguel Vences (1) , Aurélien Miralles (2) , Sophie Brouillet (2) , Jacques Ducasse , Alexander Fedosov (3) , Vladimir Kharchev (1) , Ivaylo Kostadinov , Sangeeta Kumari (1) , Stefanos Patmanidis (4) , Mark D Scherz (5) , Nicolas Puillandre (2) , Susanne S Renner

1 Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig]
2 ISYEB - Institut de Systématique, Evolution, Biodiversité
3 A.N. Severtsov Institute of Ecology and Evolution
4 NTUA - National Technical University of Athens [Athens]
5 University of Potsdam = Universität Potsdam

While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software specifically targeted at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The alpha version (iTaxoTools 0.1) distributed with this paper contains GUI versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files and tables; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses.

Mots clés: integrative taxonomy; molecular diagnosis; species delimitation; ABGD; PTP; GMYC; TR2; DELINEATE; Limes; integrative taxonomy

Domaines: Systématique, phylogénie et taxonomie

Miguel Vences, Aurélien Miralles, Sophie Brouillet, Jacques Ducasse, Alexander Fedosov, et al.. iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists. Megataxa, 2021, 6 (2), pp.77-92. ⟨10.11646/MEGATAXA.6.2.1⟩. ⟨hal-03321424⟩