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      The complete mitochondrial genome of the Atlantic spiny lumpsucker Eumicrotremus spinosus (Fabricius, 1776)

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          Abstract

          The complete mitogenome of the Atlantic spiny lumpsucker ( Eumicrotremus spinosus) was generated using the PacBio Sequel II HiFi sequencing platform. The mitogenome assembly has a length of 19,281 bp and contains 13 protein-coding sequences, 22 tRNA genes, 2 rRNA genes, one control region containing the D-loop (2383 bp) and a duplicate control region (1133 bp) Phylogenetic analysis using maximum likelihood revealed that E. spinosus is closely related to the Siberian lumpsucker ( E. asperrimus). The mitogenome of the spiny lumpsucker will be useful in population genomics and systematic studies of Cyclopteridae, Liparidae, and Cottidae.

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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.
          Article 0 comments Cited 10451 times – based on 0 reviews     Review now
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)
            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

              Bui Minh, Heiko Schmidt, Olga Chernomor … (2020)
              Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
              Article 0 comments Cited 3186 times – based on 0 reviews     Review now
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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
                Title: Mitochondrial DNA. Part B, Resources
                Publisher: Taylor & Francis
                ISSN (Electronic): 2380-2359
                Publication date (Electronic, pub): 8 March 2023
                Publication date (Electronic, collection): 2023
                Publication date PMC-release: 8 March 2023
                Volume: 8
                Issue: 3
                Pages: 364-367
                Affiliations
                [a ]Faculty of Biosciences and Aquaculture (FBA), Nord University , Bodø, Norway
                [b ]Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo , Oslo, Norway
                Author notes
                [*]

                Equal contribution.

                CONTACT Sissel Jentoft sissel.jentoft@ 123456ibv.uio.no Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo , Oslo, Norway
                Jorge M. O. Fernandes jorge.m.fernandes@ 123456nord.no Faculty of Biosciences and Aquaculture (FBA), Nord University , Bodø, Norway
                Article
                Publisher ID: 2184649
                DOI: 10.1080/23802359.2023.2184649
                PMC ID: 10013227
                PubMed ID: 36926640
                SO-VID: b2c62de9-10f5-4315-b782-88c3e1d28fa4
                Copyright © © 2023 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
                Page count
                Figures: 3, Tables: 0, Pages: 4, Words: 1647
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: cyclopteridae,e. spinosus,mitogenome,pacbio
                Data availability:
                Keywords: cyclopteridae, e. spinosus, mitogenome, pacbio

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