tag:joss.theoj.org,2005:/papers/tagged/sequence%20alignmentJournal of Open Source Software2022-03-22T13:06:50ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/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, msatag:joss.theoj.org,2005:Paper/9172019-04-30T19:09:08Z2021-02-15T11:32:26ZrGUIDANCE – alignment confidence score computation in Raccepted1.02019-03-07 04:51:37 UTC362019-04-30 19:09:08 UTC420191350Franz-SebastianKrahPlant Biodiversity Research Group, Department of Ecology & Ecosystem Management, Technical University of Munich, 85354 Freising, Germany, Bavarian Forest National Park, 94481 Grafenau, Germany0000-0001-7866-7508ChristophHeiblBavarian Forest National Park, 94481 Grafenau, Germany0000-0002-7655-329910.21105/joss.01350https://doi.org/10.5281/zenodo.2654302R, C++https://joss.theoj.org/papers/10.21105/joss.01350.pdfmultiple sequence alignment, phylogeny, genome, guide tree, R toolbox, evolutiontag:joss.theoj.org,2005:Paper/6132018-11-07T15:14:16Z2021-02-15T11:33:02Zalv: a console-based viewer for molecular sequence alignmentsacceptedv1.2.02018-09-06 07:48:11 UTC312018-11-07 15:14:16 UTC32018955LarsArvestadDepartment of Mathematics, Stockholm University, Sweden, Science for Life Laboratory, Solna, Sweden, Swedish e-science Research Centre0000-0001-5341-173310.21105/joss.00955https://doi.org/10.5281/zenodo.1477794Pythonhttps://joss.theoj.org/papers/10.21105/joss.00955.pdfbioinformatics, console, multiple sequence alignment, DNA, RNA, proteintag:joss.theoj.org,2005:Paper/3272018-01-19T16:44:00Z2021-02-15T11:33:45ZVisualizing genome synteny with xmatchviewacceptedv0.32017-12-07 23:59:55 UTC212018-01-19 16:44:00 UTC32018497RenéL.WarrenBC Cancer Agency, Genome Sciences Centre, Vancouver, BC, Canada0000-0002-9890-229310.21105/joss.00497https://doi.org/10.5281/zenodo.1155709Pythonhttps://joss.theoj.org/papers/10.21105/joss.00497.pdfGenome visualization, DNA sequence alignments, Smith Waterman Alignments, cross_match, xmatchviewtag:joss.theoj.org,2005:Paper/2022017-07-13T00:00:00Z2021-02-15T11:34:06ZKindel: indel-aware consensus for nucleotide sequence alignmentsacceptedv0.2.02017-05-26 11:32:21 UTC152017-07-13 00:00:00 UTC22017282BedeConstantinidesEvolution and Genomic Sciences, University of Manchester, Manchester, UK0000-0002-3480-3819DavidL.RobertsonMRC-University of Glasgow Centre for Virus Research, Glasgow, UK0000-0001-6338-022110.21105/joss.00282https://doi.org/10.5281/zenodo.826723Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.00282.pdfbioinformatics, sequence analysis, genome assembly