https://mapress.com/mt/issue/feed Megataxa 2021-07-23T15:54:31+12:00 Zhi-Qiang Zhang zhangz@landcareresearch.co.nz Open Journal Systems <p><strong>Megataxa</strong> is a premium open access journal for important works reporting major advances in taxonomy.</p> https://mapress.com/mt/article/view/megataxa.6.2.1 <strong>iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists</strong> 2021-06-27T19:15:13+12:00 MIGUEL VENCES m.vences@tu-braunschweig.de AURÉLIEN MIRALLES miralles.skink@gmail.com SOPHIE BROUILLET sophie.brouillet@mnhn.fr JACQUES DUCASSE jacko21@aliceadsl.fr ALEXANDER FEDOSOV fedosovalexander@gmail.com VLADIMIR KHARCHEV necrosovereign@gmail.com IVAYLO KOSTADINOV ikostadi@gfbio.org SANGEETA KUMARI kumari13@live.com STEFANOS PATMANIDIS stefanpatman91@gmail.com MARK D. SCHERZ mark.scherz@gmail.com NICOLAS PUILLANDRE nicolaspuillandre@gmail.com SUSANNE S. RENNER renner@lmu.de <p>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 targeted explicitly 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 initial version (iTaxoTools 0.1) distributed with this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains graphical user interface (GUI) versions of six species delimitation programs (<em>ABGD, ASAP, DELINEATE, GMYC, PTP, tr2</em>) 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, tables and species partition files; 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. The open source code and binaries of all tools are available from Github (https://github.com/iTaxoTools) and further information from the website (http://itaxotools.org)</p> 2021-07-23T00:00:00+12:00 Copyright (c) 2021 Magnolia Press Limited https://mapress.com/mt/article/view/megataxa.6.2.2 <p><strong>Virtual Equivalents of Real Objects (VEROs): A type of non-fungible token (NFT) that can help fund the 3D digitization of natural history collections</strong></p> 2021-07-12T11:53:46+12:00 SAMUEL J. BOLTON bolton77@googlemail.com JOSEPH R. CORA joseph.cora@nytimes.com <p>Describing a substantial proportion of the world’s species could be made much easier by the 3D digitization of collections, which would facilitate the dissemination of taxonomic information locked up in natural history museums. Three-dimensional imaging captures many characters and allows a lot of versatility in the way that morphological data is displayed and used (Wheeler <em>et al.</em> 2012; Faulwetter <em>et al.</em> 2013). Moreover, the loss and damage of valuable specimens, many of which are very fragile, can be reduced as a result of the use and sharing of 3D model substitutes among researchers. This can also lead to a reduction in the handling and transportation expenses of many specimens.</p> 2021-08-04T00:00:00+12:00 Copyright (c) 2021 Magnolia Press Limited