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      A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam

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          Most cited references 63

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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            Basic local alignment search tool.

            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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              Is Open Access

              IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

              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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                Author and article information

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                Journal
                Journal of Natural History
                Journal of Natural History
                Informa UK Limited
                0022-2933
                1464-5262
                October 17 2020
                March 19 2021
                October 17 2020
                : 54
                : 39-40
                : 2543-2575
                Affiliations
                [1 ]Zoological Society of London, London, UK
                [2 ]Australian Museum Research Institute, Australian Museum, Sydney, Australia
                [3 ]Indo-Myanmar Conservation, London, UK
                [4 ]EDGE of Existence Programme, Zoological Society of London, London, UK
                [5 ]School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
                [6 ]Department of Life Sciences, The Natural History Museum, London, UK
                [7 ]Hoang Lien National Park, Lao Cai, Vietnam
                [8 ]Wild Planet Trust, Paignton, UK
                [9 ]Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
                Article
                10.1080/00222933.2020.1856952
                1b0df51e-f157-4206-a5a8-f69736d1709e
                © 2020

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