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QualitySNPng: a user-friendly SNP detection and visualization tool.

Nijveen H, van Kaauwen M, Esselink DG, Hoegen B, Vosman B.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W587-90. doi: 10.1093/nar/gkt333. Epub 2013 Apr 30.


QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species.

Tang J, Vosman B, Voorrips RE, van der Linden CG, Leunissen JA.

BMC Bioinformatics. 2006 Oct 9;7:438.


SNP-VISTA: an interactive SNP visualization tool.

Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, Dubchak IL.

BMC Bioinformatics. 2005 Dec 8;6:292.


SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.

Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.

BMC Bioinformatics. 2011 May 5;12:134. doi: 10.1186/1471-2105-12-134.


SNP-PHAGE--High throughput SNP discovery pipeline.

Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, Van Tassell CP.

BMC Bioinformatics. 2006 Oct 23;7:468.


HaploSNPer: a web-based allele and SNP detection tool.

Tang J, Leunissen JA, Voorrips RE, van der Linden CG, Vosman B.

BMC Genet. 2008 Feb 28;9:23. doi: 10.1186/1471-2156-9-23.


An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.

Azam S, Rathore A, Shah TM, Telluri M, Amindala B, Ruperao P, Katta MA, Varshney RK.

PLoS One. 2014 Jul 8;9(7):e101754. doi: 10.1371/journal.pone.0101754. eCollection 2014.


RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics.

Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7. doi: 10.1093/nar/gks540. Epub 2012 Jun 8.


SNPsyn: detection and exploration of SNP-SNP interactions.

Curk T, Rot G, Zupan B.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W444-9. doi: 10.1093/nar/gkr321. Epub 2011 May 16.


CGHPRO -- a comprehensive data analysis tool for array CGH.

Chen W, Erdogan F, Ropers HH, Lenzner S, Ullmann R.

BMC Bioinformatics. 2005 Apr 5;6:85.


MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation.

Hou H, Zhao F, Zhou L, Zhu E, Teng H, Li X, Bao Q, Wu J, Sun Z.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W732-6. doi: 10.1093/nar/gkq302. Epub 2010 May 5.


Seq-SNPing: multiple-alignment tool for SNP discovery, SNP ID identification, and RFLP genotyping.

Chang HW, Chuang LY, Cheng YH, Ho CH, Wen CH, Yang CH.

OMICS. 2009 Jun;13(3):253-60. doi: 10.1089/omi.2008.0058.


Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing.

Koepke T, Schaeffer S, Krishnan V, Jiwan D, Harper A, Whiting M, Oraguzie N, Dhingra A.

BMC Genomics. 2012 Jan 12;13:18. doi: 10.1186/1471-2164-13-18.


WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations.

Wangkumhang P, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, Assawamakin A, Tongsima S.

BMC Genomics. 2007 Aug 14;8:275.


BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.

Yuan Y, Norris C, Xu Y, Tsui KW, Ji Y, Liang H.

BMC Genomics. 2012;13 Suppl 8:S9. doi: 10.1186/1471-2164-13-S8-S9. Epub 2012 Dec 17.


Flapjack--graphical genotype visualization.

Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas WT, Flavell AJ, Marshall D.

Bioinformatics. 2010 Dec 15;26(24):3133-4. doi: 10.1093/bioinformatics/btq580. Epub 2010 Oct 18.


HaploPainter: a tool for drawing pedigrees with complex haplotypes.

Thiele H, Nürnberg P.

Bioinformatics. 2005 Apr 15;21(8):1730-2. Epub 2004 Sep 17.


SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.

Panitz F, Stengaard H, Hornshøj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Høj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jørgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C.

Bioinformatics. 2007 Jul 1;23(13):i387-91.


Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence.

You FM, Huo N, Deal KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OD.

BMC Genomics. 2011 Jan 25;12:59. doi: 10.1186/1471-2164-12-59.


High-throughput identification, database storage and analysis of SNPs in EST sequences.

Useche FJ, Gao G, Harafey M, Rafalski A.

Genome Inform. 2001;12:194-203.

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