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      Genomic landscape of the global oak phylogeny

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          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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            APE: Analyses of Phylogenetics and Evolution in R language.

            Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
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              BLAST+: architecture and applications

              Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.
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                Author and article information

                Journal
                New Phytologist
                New Phytol
                Wiley
                0028-646X
                1469-8137
                October 14 2019
                October 14 2019
                Affiliations
                [1 ]The Morton Arboretum Lisle IL 60532‐1293USA
                [2 ]The Field Museum Chicago IL 60605 USA
                [3 ]Duke University Durham NC 27708 USA
                [4 ]Previously of The Hebrew University of Jerusalem Botanical Garden Zalman Shne'ur St. 1 Jerusalem Israel
                [5 ]INRA UMR1202 BIOGECO Cestas F‐33610 France
                [6 ]University of Minnesota Minneapolis MN 55455 USA
                [7 ]Shanghai Chenshan Plant Science Research Center Chinese Academy of Sciences Shanghai 201602 China
                [8 ]Swedish Museum of Natural History Stockholm 10405 Sweden
                [9 ]University of California, Los Angeles Los Angeles CA 90095 USA
                [10 ]Büsgen‐Institute Georg‐August‐University Göttingen Göttingen D‐37077 Germany
                [11 ]CIIDIR Unidad Durango Instituto Politécnico Nacional Durango 34220 México
                [12 ]Escuela Nacional de Estudios Superiores Unidad Morelia Universidad Nacional Autónoma de México Morelia 58190 México
                [13 ]Orléans 45100 France
                [14 ]Max Planck Institute for Biogeochemistry Hans‐Knoell‐Str. 10 Jena 07745 Germany
                [15 ]Università degli Studi della Tuscia Viterbo 01100 Italy
                [16 ]Herbario de la Facultad de Ciencias Departamento de Biología Comparada Universidad Nacional Autónoma de México Circuito Exterior, s.n., Ciudad Universitaria, Coyoacán México City CP 04510 México
                Article
                10.1111/nph.16162
                © 2019

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

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