tag:joss.theoj.org,2005:/papers/reviewed_by/@standageJournal of Open Source Software2022-04-25T13:43:17ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/34002022-04-25T13:43:17Z2022-04-26T00:00:54ZPyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotesacceptedv0.6.42022-02-25 23:49:54 UTC722022-04-25 13:43:17 UTC720224296MartinLarraldeStructural and Computational Biology Unit, EMBL, Heidelberg, Germany0000-0002-3947-444410.21105/joss.04296https://doi.org/10.5281/zenodo.6472583Python, C, Cythonhttps://joss.theoj.org/papers/10.21105/joss.04296.pdfbioinformatics, gene predictiontag:joss.theoj.org,2005:Paper/27392021-08-22T19:59:26Z2021-08-23T02:13:38ZOSTIR: open source translation initiation rate predictionacceptedv1.0.42021-06-08 03:04:25 UTC642021-08-22 19:59:26 UTC620213362CameronT.RootsDepartment of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin0000-0001-6219-3168AlexandraLukasiewiczMcKetta Department of Chemical Engineering, The University of Texas at AustinJeffreyE.BarrickDepartment of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin0000-0003-0888-735810.21105/joss.03362https://doi.org/10.5281/zenodo.5227845R, Pythonhttps://joss.theoj.org/papers/10.21105/joss.03362.pdfsynthetic biology, systems biology, bioengineering, ribosome binding site, translation, calculatortag:joss.theoj.org,2005:Paper/14152020-02-04T14:47:33Z2021-02-15T11:31:13ZReferenceSeeker: rapid determination of appropriate reference genomesacceptedv1.42019-12-19 18:33:52 UTC462020-02-04 14:47:33 UTC520201994OliverSchwengersBioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, 35392, Germany, Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, 35392, Germany, German Centre for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany0000-0003-4216-2721TorstenHainInstitute of Medical Microbiology, Justus Liebig University Giessen, Giessen, 35392, Germany, German Centre for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, GermanyTrinadChakrabortyInstitute of Medical Microbiology, Justus Liebig University Giessen, Giessen, 35392, Germany, German Centre for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, GermanyAlexanderGoesmannBioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, 35392, Germany, German Centre for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany0000-0002-7086-256810.21105/joss.01994https://doi.org/10.5281/zenodo.3635630Pythonhttps://joss.theoj.org/papers/10.21105/joss.01994.pdfBioinformatics, WGS, NGS, Microbiologytag:joss.theoj.org,2005:Paper/14132020-01-16T19:12:12Z2021-02-15T11:31:13ZDNAtools: Tools for Analysing Forensic Genetic DNA Dataaccepted0.2-12019-12-19 09:36:15 UTC452020-01-16 19:12:12 UTC520201981TorbenTvedebrinkDepartment of Mathematical Sciences, Aalborg University, Denmark0000-0002-9292-8476MikkelMeyerAndersenDepartment of Mathematical Sciences, Aalborg University, Denmark0000-0002-0234-0266JamesMichaelCurranDepartment of Statistics, University of Auckland, New Zealand0000-0003-3323-673310.21105/joss.01981https://doi.org/10.5281/zenodo.3609584R, C++https://joss.theoj.org/papers/10.21105/joss.01981.pdfshort tandem repeat markers, forensic genetics, autosomal markers, population genetics, weight of evidencetag:joss.theoj.org,2005:Paper/12262019-12-10T18:30:45Z2021-02-15T11:31:35ZMashtree: a rapid comparison of whole genome sequence filesacceptedv0.572019-09-18 20:34:06 UTC442019-12-10 18:30:45 UTC420191762LeeS.KatzEnteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA, Center for Food Safety, University of Georgia, Griffin, GA, USA0000-0002-2533-9161TaylorGriswoldEnteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USAShataviaS.MorrisonRespiratory Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA0000-0002-4658-5951JasonA.CaravasRespiratory Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA0000-0001-9111-406XShaokangZhangCenter for Food Safety, University of Georgia, Griffin, GA, USA0000-0003-0874-2212HenkC. denBakkerCenter for Food Safety, University of Georgia, Griffin, GA, USA0000-0002-4086-1580XiangyuDengCenter for Food Safety, University of Georgia, Griffin, GA, USAHeatherA.CarletonEnteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA10.21105/joss.01762https://doi.org/10.5281/zenodo.3568386Perlhttps://joss.theoj.org/papers/10.21105/joss.01762.pdfdendrogram, mash, sketch, tree, rapid