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      Phylogenomics and species delimitation for effective conservation of manta and devil rays

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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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            The variant call format and VCFtools

            Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk
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              jModelTest 2: more models, new heuristics and parallel computing.

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                Author and article information

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                Journal
                Molecular Ecology
                Mol Ecol
                Wiley
                0962-1083
                1365-294X
                November 09 2020
                Affiliations
                [1 ]Molecular Ecology and Fisheries Genetics Laboratory Bangor University Bangor UK
                [2 ]The Manta Trust Catemwood House, Norwood Lane Corscombe Dorset DT2 0NT UK
                [3 ]NERC Biomolecular Analysis Facility Department of Animal and Plant Sciences University of Sheffield Sheffield UK
                [4 ]Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Edinburgh UK
                [5 ]TRACE Wildlife Forensics Network Edinburgh UK
                [6 ]School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
                [7 ]National Research Center Gaza City Palestine
                [8 ]Mote Marine Laboratory The Center for Shark Research Sarasota FL USA
                [9 ]Océanos Vivientes A. C. Mexico City Mexico
                [10 ]Department of Biology and Environmental Science Linnaeus University Kalmar Sweden
                [11 ]Blue Resources Trust Colombo Sri Lanka
                [12 ]Department of Natural History Norwegian University of Science and Technology (NTNU) University Museum Trondheim Norway
                [13 ]Elasmo Project Dubai UAE
                [14 ]RZSS WildGenes Lab Royal Zoological Society of Scotland Edinburgh UK
                [15 ]WWF Pakistan Karachi Pakistan
                [16 ]School of Biological Sciences University of Western Australia Crawley WA Australia
                [17 ]The Australian Institute of Marine Science Crawley WA Australia
                [18 ]Save Our Seas Foundation – D'Arros Research Centre Geneva Switzerland
                [19 ]Large Marine Vertebrates Research Institute Philippines Jagna Philippines
                [20 ]Tolheksbos 57 Hoofddorp 2134 GH The Netherlands
                [21 ]Ministry of Agriculture Directorate General of Fisheries Gaza City Palestine
                [22 ]KwaZulu‐Natal Sharks Board Umhlanga Rocks South Africa
                [23 ]School of Life Sciences University of KwaZulu‐Natal Durban South Africa
                Article
                10.1111/mec.15683
                © 2020

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