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      Complete chloroplast genome sequence of Ampelocalamus scandens (Arundinarodae)

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          Abstract

          Ampelocalamus scandens is native to Guizhou Province, China, and grows at an altitude of 260–320 m. It can be used as a raw material for weaving and papermaking. In the current study, the complete chloroplast (cp) genome of A. scandens was sequenced and is reported for the first time. The complete cp sequence was 139,504 bp, include large single-copy (LSC), small single-copy (SSC), and a pair of invert repeats (IR) region of 83,103 bp, 12,813 bp, and 21,793 bp, respectively. Besides, the plastid genome comprised a total of 132 genes, including protein-coding, tRNA, and rRNA genes as 85, 39, and 8 genes, respectively. Phylogenetic analysis based on 28 cp genomes reveals that A. scandens is closely associated with Ampelocalamus melicoideus in Arundinarodae.

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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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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Alexandros Stamatakis (2014)
            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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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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                Author and article information

                Journal
                Journal ID (nlm-ta): Mitochondrial DNA B Resour
                Journal ID (iso-abbrev): Mitochondrial DNA B Resour
                Journal ID (publisher-id): TMDN
                Journal ID (publisher-id): tmdn20
                Title: Mitochondrial DNA. Part B, Resources
                Publisher: Taylor & Francis
                ISSN (Electronic): 2380-2359
                Publication date Collection: 2020
                Publication date (Electronic): 01 June 2020
                Volume: 5
                Issue: 3
                Pages: 2237-2238
                Affiliations
                [a ]College of Forestry, Fujian Agriculture and Forestry University , Fuzhou, PR China;
                [b ]College of Landscape, Fujian Agriculture and Forestry University , Fuzhou, PR China;
                Author notes
                CONTACT Yu-Shan Zheng zys1960@ 123456163.com College of Forestry, Fujian Agriculture and Forestry University , Fuzhou, PR China; College of Arts & College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou, Fujian, PR China; Key Laboratory of Bamboo Institute at College of Forestry , Fuzhou, PR China
                Author information
                http://orcid.org/0000-0001-9673-0881
                http://orcid.org/0000-0003-2055-4185
                http://orcid.org/0000-0001-7636-3893
                http://orcid.org/0000-0002-7300-2539
                http://orcid.org/0000-0002-8733-8500
                http://orcid.org/0000-0001-9545-0984
                Article
                Publisher ID: 1768939
                DOI: 10.1080/23802359.2020.1768939
                PMC ID: 7510662
                SO-VID: 346d7acd-14d8-436e-8eae-e23e0f046111
                Copyright © © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 02 May 2020
                Date accepted : 09 May 2020
                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 1054
                Funding
                This work was supported by the Regional Development Project of Fujian Province (2015, No.3015), Research Development Fund of Fujian Agriculture and Forestry University [KF2015085 and CXZX2017119], Program for Scientific and Technological Innovation Team for Universities of Fujian Province (2018, No.49), Science and Technology Innovation and Development Fund Project of Fujian Agriculture and Forestry University (CXZX2017118), and Major Science and Technology Project of Fujian Province (2013NZ0001).
                Categories
                Subject: Mitogenome Announcement

                Keywords: ampelocalamus scandens,plastid genome,phylogeny,arundinarodae
                Data availability:
                Keywords: ampelocalamus scandens, plastid genome, phylogeny, arundinarodae

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