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      Ameripathidae, a new family of antipatharian corals (Cnidaria, Anthozoa, Hexacorallia, Antipatharia)

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          Abstract

          A new family of antipatharian corals, Ameripathidae ( Cnidaria : Anthozoa : Antipatharia ), is established for Ameripathes pseudomyriophylla Opresko & Horowitz, gen. et sp. nov. The new family resembles Myriopathidae and Stylopathidae in terms of the morphology of the polyps and tentacles and the pinnulate branching of the corallum. Phylogenetic analysis using a genomic data set of 741 conserved element loci indicates that the new family is sister to a clade containing the Myriopathidae , Stylopathidae , Antipathidae , and Aphanipathidae .

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)
          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

            Kazutaka Katoh, Daron Standley (2013)
            We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Subha Kalyaanamoorthy, Bui Minh, Thomas Wong … (2017)
              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
              Article 0 comments Cited 4205 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Jeremy Horowitz:
                ORCID: https://orcid.org/0000-0002-2643-5200
                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: 2024
                Publication date (Electronic): 31 May 2024
                Volume: 1203
                Pages: 355-375
                Affiliations
                [1 ] Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA National Museum of Natural History, Smithsonian Institution Washington DC United States of America
                [2 ] Department of Biological Sciences, Lehigh University, Lehigh, PA, USA Lehigh University Lehigh United States of America
                [3 ] Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA Woods Hole Oceanographic Institution Woods Hole United States of America
                Author notes
                Corresponding author: Jeremy Horowitz ( Jerhorowitz@ 123456gmail.com)

                Academic editor: Bert W. Hoeksema

                Author information
                https://orcid.org/0000-0002-2643-5200
                https://orcid.org/0000-0001-9946-1533
                https://orcid.org/0000-0001-7204-9434
                https://orcid.org/0000-0002-3506-7710
                https://orcid.org/0000-0002-4247-3055
                Article
                Publisher ID: 121411
                DOI: 10.3897/zookeys.1203.121411
                PMC ID: 11161683
                PubMed ID: 38855792
                SO-VID: 73487612-9239-4f18-bd35-7549ec723f66
                License:

                This is an open access article distributed under the terms of the CC0 Public Domain Dedication.

                History
                Date received : 21 February 2024
                Date accepted : 16 April 2024
                Categories
                Subject: Research Article
                Subject: Antipatharia
                Subject: Taxonomy
                Subject: Central America and the Caribbean

                ScienceOpen disciplines: Animal science & Zoology
                Keywords: deep sea,fauna of puerto rico,genome skimming,mesophotic,molecular phylogenetics,new genus,new species,taxonomy,ultraconserved elements
                Data availability:
                ScienceOpen disciplines: Animal science & Zoology
                Keywords: deep sea, fauna of puerto rico, genome skimming, mesophotic, molecular phylogenetics, new genus, new species, taxonomy, ultraconserved elements

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