title: MEvoLib v1.0: the first molecular evolution library for Python.
abstract: 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.
authors: Depto. de Informática e Ingeniería de Sistemas (DIIS), Universidad de Zaragoza, María de Luna 1, Zaragoza, 50018, Spain. jorgeal@unizar.es.|Instituto de Investigación en Ingeniería de Aragón (I3A), Universidad de Zaragoza, Mariano Esquillor s/n, Zaragoza, 50018, Spain. jorgeal@unizar.es.
authors: Jorge
authors: http://orcid.org/0000-0002-0946-0957
authors: J
authors: Álvarez-Jarreta
authors: Depto. de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Miguel Server 177, Zaragoza, 50013, Spain.|Instituto de Investigación Sanitaria de Aragón (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain.|CIBER de enfermedades raras, Instituto de Salud Carlos III, Monforte de Lemos 5, Madrid, 28029, Spain.|Fundación ARAID, María de Luna 11, Zaragoza, 50018, Spain.
authors: Eduardo
authors: E
authors: Ruiz-Pesini
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D015723:Gene Library; D005796:Genes; D006801:Humans; D012984:Software
chemical_list: D004272:DNA, Mitochondrial
keywords: Biological knowledge; Molecular evolution; Multiple sequence alignment; Phylogenetic inference; Python; Software; Supertrees