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      Scale(s) matter: Deconstructing an area of endemism for Middle American freshwater fishes

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          Is Open Access

          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          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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            Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

            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

              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
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                Journal
                Journal of Biogeography
                J Biogeogr
                Wiley
                0305-0270
                1365-2699
                November 2020
                August 30 2020
                November 2020
                : 47
                : 11
                : 2483-2501
                Affiliations
                [1 ]LSU Museum of Natural Science (Ichthyology section) Department of Biological Sciences Louisiana State University Baton Rouge LA USA
                [2 ]Field Museum of Natural History Chicago IL USA
                [3 ]Museo de Zoología Instituto de Ciencias Biológicas Universidad de Ciencias y Artes de Chiapas Tuxtla Gutiérrez Chiapas México
                [4 ]Department of Biological Sciences Southeastern Louisiana University Hammond LA USA
                Article
                10.1111/jbi.13941
                db9ae31c-7c61-4c25-a97a-bf608fa06e24
                © 2020

                http://onlinelibrary.wiley.com/termsAndConditions#am

                http://onlinelibrary.wiley.com/termsAndConditions#vor

                http://doi.wiley.com/10.1002/tdm_license_1.1


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