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      A troglobitic species of the centipede Cryptops (Chilopoda, Scolopendromorpha) from northwestern Botswana

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          Abstract

          A new species of Cryptops , C. ( Cryptops) legagus sp. nov., occurs in caves in the Koanaka and Gcwihaba Hills in northwestern Botswana. Bayesian molecular phylogenetics using 18S rRNA, 28S rRNA, 16S rRNA and cytochrome c oxidase subunit I corroborates a morphological assignment to the subgenus Cryptops and closest affinities to southern temperate species in South Africa, Australia and New Zealand. The new species is not conspicuously modified as a troglomorph.

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          Basic local alignment search tool.

          Stephen F Altschul, Warren Gish, Webb Miller … (1990)
          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

            Matthew Kearse, Richard Moir, Amy Wilson … (2012)
            Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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              Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

              Andrew Rambaut, Alexei J. Drummond, Dong Xie … (2018)
              Abstract Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.
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                Author and article information

                Contributors
                Gregory D. Edgecombe
                Journal
                Journal ID (nlm-ta): Zookeys
                Journal ID (iso-abbrev): Zookeys
                Journal ID (publisher-id): 2
                Journal ID (index): urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                Journal ID (aggregator): urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                Title: ZooKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1313-2989
                ISSN (Electronic): 1313-2970
                Publication date Collection: 2020
                Publication date (Electronic): 22 October 2020
                Volume: 977
                Pages: 25-40
                Affiliations
                [1 ] The Natural History Museum, Cromwell Road, London SW7 5BD, UK The Natural History Museum London United Kingdom
                [2 ] Naturhistorisches Museum Wien, Burgring 7, 1010 Wien, Austria Naturhistorisches Museum Wien Wien Austria
                [3 ] Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa North-West University Potchefstroom South Africa
                Author notes
                Corresponding author: Gregory D. Edgecombe ( g.edgecombe@ 123456nhm.ac.uk )

                Academic editor: Pavel Stoev

                Author information
                https://orcid.org/0000-0001-5019-4833
                Article
                Publisher ID: 57088
                DOI: 10.3897/zookeys.977.57088
                PMC ID: 7596027
                SO-VID: ad8b6f40-d278-4c63-a8e6-46cbb3a298f3
                Copyright © Gregory D. Edgecombe, Nesrine Akkari, Edward C. Netherlands, Gerhard Du Preez
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 30 July 2020
                Date accepted : 04 September 2020
                Categories
                Subject: Research Article
                Subject: Animalia
                Subject: Chilopoda
                Subject: Systematics
                Subject: Africa

                ScienceOpen disciplines: Animal science & Zoology
                Keywords: biospeleology, cryptopidae ,molecular phylogenetics
                Data availability:
                ScienceOpen disciplines: Animal science & Zoology
                Keywords: biospeleology, cryptopidae , molecular phylogenetics

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