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      Global diversity and distribution of close relatives of apicomplexan parasites : Diversity and distribution of apicomplexan parasites

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          QIIME allows analysis of high-throughput community sequencing data.

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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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              Is Open Access

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

              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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                Author and article information

                Journal
                Environmental Microbiology
                Environ Microbiol
                Wiley
                14622912
                August 2018
                August 2018
                June 01 2018
                : 20
                : 8
                : 2824-2833
                Affiliations
                [1 ]Department of Botany; University of British Columbia; Vancouver British Columbia Canada
                [2 ]Department of Marine Biology and Oceanography; Institut de Ciències del Mar (CSIC); Barcelona Spain
                [3 ]Institute of Parasitology, Biology Centre, Czech Academy of Sciences; Branišovská 31, 370 05 České Budějovice, Czech Republic
                Article
                10.1111/1462-2920.14134
                © 2018

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

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

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