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

Bioinformatics - Tập 30 Số 9 - Trang 1312-1313 - 2014
Alexandros Stamatakis1
11 Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg and 2Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany

Tóm tắt

Abstract 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:  [email protected] Supplementary information:  Supplementary data are available at Bioinformatics online.

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Thông tin xuất bản

Bioinformatics

Tập 30 Số 9

1312-1313

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