57763 20200221144223.0 doi 10.1186/s12859-016-1303-3 sideral 96984 ART-2016-96984 eng (orcid)0000-0002-0946-0957 Álvarez-Jarreta, J. Universidad de Zaragoza MEvoLib v1.0: The first molecular evolution library for Python 2016 Access copy available to the general public Unrestricted Background: Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow. Results: We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows. In contrast with already existing bioinformatics libraries, MEvoLib is focused on the stages involved in molecular evolution studies, enclosing the set of tools with a common purpose in a single high-level interface with fast access to their frequent parameterizations. The gene clustering from partial or complete sequences has been improved with a new method that integrates accessible external information (e.g. GenBank''s features data). Moreover, MEvoLib adjusts the fetching process from NCBI databases to optimize the download bandwidth usage. In addition, it has been implemented using parallelization techniques to cope with even large-case scenarios. Conclusions: MEvoLib is the first library for Python designed to facilitate molecular evolution researches both for expert and novel users. Its unique interface for each common task comprises several tools with their most used parameterizations. It has also included a method to take advantage of biological knowledge to improve the gene partition of sequence datasets. Additionally, its implementation incorporates parallelization techniques to enhance computational costs when handling very large input datasets. info:eu-repo/grantAgreement/ES/MINECO/TIN2011-27479-C04-01 info:eu-repo/grantAgreement/ES/MEC/FPU-AP2010-1058 info:eu-repo/grantAgreement/ES/FIS/PI14-00070 info:eu-repo/grantAgreement/ES/DGA/T27 info:eu-repo/grantAgreement/ES/DGA/B33 info:eu-repo/semantics/openAccess by http://creativecommons.org/licenses/by/3.0/es/ 2.448 2016 MATHEMATICAL & COMPUTATIONAL BIOLOGY 10 / 57 = 0.175 2016 Q1 T1 BIOCHEMICAL RESEARCH METHODS 38 / 77 = 0.494 2016 Q2 T2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY 67 / 160 = 0.419 2016 Q2 T2 1.581 2016 Applied Mathematics 2016 Q1 Biochemistry 2016 Q1 Computer Science Applications 2016 Q1 Molecular Biology 2016 Q2 Structural Biology 2016 Q2 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion (orcid)0000-0002-0269-7337 Ruiz-Pesini, E. Universidad de Zaragoza 1002 060 Universidad de Zaragoza Dpto. Bioq.Biolog.Mol. Celular Área Bioquímica y Biolog.Mole. 5007 570 Universidad de Zaragoza Dpto. Informát.Ingenie.Sistms. Área Lenguajes y Sistemas Inf. 17, 436 (2016), [8 pp.] BMC bioinformatics BMC BIOINFORMATICS 1471-2105 540528 http://zaguan.unizar.es/record/57763/files/texto_completo.pdf Versión publicada 11082 http://zaguan.unizar.es/record/57763/files/texto_completo.jpg?subformat=icon icon Versión publicada oai:zaguan.unizar.es:57763 articulos driver 2020-02-21-13:16:29 ARTICLE