tag:joss.theoj.org,2005:/papers/tagged/aliensJournal of Open Source Software2023-05-15T11:55:06ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/42192023-05-15T11:55:06Z2023-05-16T00:01:31Zrepytah: An Open-Source Python Package for Building Aligned Hierarchies for Sequential Dataacceptedv0.1.02023-02-17 17:12:42 UTC852023-05-15 11:55:06 UTC820235213ChenhuiJiaSmith College, USALizetteCarpenterSmith College, USAThuTranSmith College, USAAmandaY.LiuSmith College, USASashaYeutseyevaSmith College, USAMariumTapalSmith College, USA0000-0001-5093-6462YingkeWangColumbia University, USAZoieKexinZhaoSmith College, USAJordanMoodySmith College, USADeniseNavaSmith College, USAEleanorDonaherSmith College, USALillianYushuJiangSmith College, USABenBruncatiSmith College, USAKatherineM.KinnairdSmith College, USA0000-0002-0435-899610.21105/joss.05213https://doi.org/10.5281/zenodo.7931423Pythonhttps://joss.theoj.org/papers/10.21105/joss.05213.pdfMusic Information Retrieval, Structure representations, Aligned Hierarchies, Music Structure Analysistag:joss.theoj.org,2005:Paper/33412022-12-28T08:58:46Z2022-12-29T00:01:19ZRedOak: a reference-free and alignment-free structure for indexing a collection of similar genomesaccepted0.1.42022-02-15 13:53:48 UTC802022-12-28 08:58:46 UTC720224363ClémentAgretLIRMM, Univ Montpellier, CNRS, Montpellier, France, Cirad, UMR AGAP, Avenue Agropolis, Montpellier, France, CRIStAL, Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France0000-0002-7404-7253AnnieChateauLIRMM, Univ Montpellier, CNRS, Montpellier, France, Institut de Biologie Computationnelle, Montpellier, France0000-0003-4760-8171GaetanDrocCirad, UMR AGAP, Avenue Agropolis, Montpellier, France0000-0003-1849-1269GautierSarahINRA, UMR AGAP, 2 Place Pierre Viala, Montpellier, France0000-0001-5179-972XManuelRuizCirad, UMR AGAP, Avenue Agropolis, Montpellier, France, Institut de Biologie Computationnelle, Montpellier, France0000-0001-8153-276XAlbanMancheronLIRMM, Univ Montpellier, CNRS, Montpellier, France, Institut de Biologie Computationnelle, Montpellier, France0000-0001-9249-759210.21105/joss.04363https://doi.org/10.6084/m9.figshare.21711767M4, Chttps://joss.theoj.org/papers/10.21105/joss.04363.pdfC/C++, Bioinformatic, k-mers, Genomes, Indextag:joss.theoj.org,2005:Paper/35112022-06-01T20:05:57Z2022-06-02T00:01:04Zsam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment filesacceptedv1.0.0b2022-04-21 15:14:38 UTC742022-06-01 20:05:57 UTC720224360MaximeBorryMicrobiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany0000-0001-9140-7559AlexanderHübnerMicrobiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany, Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany0000-0003-3572-9996ChristinaWarinnerMicrobiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany, Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany, Department of Anthropology, Harvard University, Cambridge, MA, United States of America0000-0002-4528-587710.21105/joss.04360https://doi.org/10.5281/zenodo.6585307Pythonhttps://joss.theoj.org/papers/10.21105/joss.04360.pdfmetagenomics, microbiome, alignment, sam, bam, cram, htslib, taxonomy, LCA, ancestortag:joss.theoj.org,2005:Paper/32002022-03-22T13:06:50Z2022-03-23T00:00:48Zhelayo: Reconstructing Sanskrit texts from manuscript witnessesacceptedv0.5 (helayo) v0.8 (matrix editor)2021-12-01 14:16:58 UTC712022-03-22 13:06:50 UTC720224022CharlesLiCentre nationale de la recherche scientifique, École des hautes études en sciences sociales0000-0001-8247-937410.21105/joss.04022https://doi.org/10.5281/zenodo.6334073Haskell, JavaScript, XSLThttps://joss.theoj.org/papers/10.21105/joss.04022.pdfJavascript, critical editing, philology, Sanskrit, sequence alignmenttag:joss.theoj.org,2005:Paper/30132021-11-30T18:19:17Z2021-12-01T00:02:35ZNextclade: clade assignment, mutation calling and quality control for viral genomesacceptedv1.3.02021-09-03 13:36:34 UTC672021-11-30 18:19:17 UTC620213773IvanAksamentovBiozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0002-7557-9673CorneliusRoemerBiozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0002-6138-6539EmmaB.HodcroftSwiss Institute of Bioinformatics, Basel, Switzerland, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland0000-0002-0078-2212RichardA.NeherBiozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0003-2525-140710.21105/joss.03773https://doi.org/10.5281/zenodo.5726681Ruby, C++https://joss.theoj.org/papers/10.21105/joss.03773.pdfphylogenetics, typing, sequence alignmenttag:joss.theoj.org,2005:Paper/28162021-08-20T20:59:21Z2021-08-21T00:00:36ZThe MarINvaders Toolkitacceptedv0.3.12021-06-23 12:41:05 UTC642021-08-20 20:59:21 UTC620213575RadekLonkaIndustrial Ecology Programme, NTNU Trondheim, Norway.0000-0002-5815-8682FrancescaVeronesIndustrial Ecology Programme, NTNU Trondheim, Norway.0000-0002-2908-328XKonstantinStadlerIndustrial Ecology Programme, NTNU Trondheim, Norway.0000-0002-1548-201X10.21105/joss.03575https://doi.org/10.5281/zenodo.4621392Python, Roffhttps://joss.theoj.org/papers/10.21105/joss.03575.pdfinvasive species, marine biodiversity, ecosystems, alienstag:joss.theoj.org,2005:Paper/16882020-11-15T18:30:52Z2021-02-15T11:30:38ZCRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in Racceptedv0.0.12020-05-26 15:41:11 UTC552020-11-15 18:30:52 UTC520202424KristianK.UllrichMax Planck Institute for Evolutionary Biology, Scientific IT group, August Thienemann Str. 2, 24306 Plön0000-0003-4308-962610.21105/joss.02424https://doi.org/10.5281/zenodo.4247942R, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.02424.pdfreciprocal best hit, conditional reciprocal best hit, codon alignment, Ka/Ks, dN/dS, tandem duplicated genes, syntenytag:joss.theoj.org,2005:Paper/18112020-09-23T23:57:46Z2022-01-18T11:38:56ZChromatiblock: scalable whole-genome visualization of structural differences in prokaryotesacceptedv0.4.22020-07-01 04:17:07 UTC532020-09-23 23:57:46 UTC520202451MitchellJohnSullivanDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of AmericaHarmvan BakelDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America10.21105/joss.02451https://doi.org/10.5281/zenodo.4034604Pythonhttps://joss.theoj.org/papers/10.21105/joss.02451.pdfBioinformatics, Microbial genomics, Visualization, multiple alignmenttag:joss.theoj.org,2005:Paper/11402019-10-08T22:15:08Z2022-01-18T11:27:02ZSpruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignmentsacceptedv2019.1.12019-07-31 15:43:35 UTC422019-10-08 22:15:08 UTC420191635MarekL.BorowiecDepartment of Entomology, Plant Pathology and Nematology, University of Idaho10.21105/joss.01635https://doi.org/10.5281/zenodo.3476875Pythonhttps://joss.theoj.org/papers/10.21105/joss.01635.pdfbioinformatics, alignment trimming, phylogenetics, orthologytag:joss.theoj.org,2005:Paper/9592019-07-10T12:54:57Z2021-02-15T11:32:18ZLexicon-Mono-Seq, DOM Text Based Async MSA Vieweracceptedv0.15.122019-04-12 13:20:54 UTC392019-07-10 12:54:57 UTC420191407IbrahimTanyalcinVrije Universiteit Brussel0000-0003-0327-509610.21105/joss.01407https://doi.org/10.5281/zenodo.3273310JavaScripthttps://joss.theoj.org/papers/10.21105/joss.01407.pdfES5, async, requestAnimationFrame, js, BioJs, Bionode, alignment, sequence, bioinformatics, msa