CodonCode Aligner

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CodonCode Aligner
Developer(s) CodonCode Corporation
Stable release
4.2.5 / 2013
Operating system Mac OS X, WIndows
Type Bioinformatics
License commercial; free for limited use (trace viewing & editing)

CodonCode Aligner is a commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows.


Features include chromatogram editing, end clipping, and vector trimming, sequence assembly and contig editing, aligning cDNA against genomic templates, sequence alignment and editing, alignment of contigs to each other with ClustalW, MUSCLE, or built-in algorithms, mutation detection, including detection of heterozygous single-nucleotide polymorphism, analysis of heterozygous insertions and deletions, start online BLAST searches, restriction analysis (find and view restriction cut sites), trace sharpening, and support for Phred, Phrap, ClustalW, and MUSCLE.


The first beta version of CodonCode Aligner was released in April 2003, followed by the first full version in June 2003. Major upgrades were released in 2003, 2004, 2005, 2006, 2007, and 2008.

In April 2009, CodonCode Aligner had been cited in more than 400 scientific publications. Citations cover a wide variety of biomedical research areas, including HIV research,[1][2][3] biogeography and environmental biology,[4][5] DNA methylation studies,[6] genetic diseases,[7][8][9] clinical microbiology,[10][11] and evolution research and phylogenetics.[12][13][14]

See also[edit]


  1. ^ Bailey JR, Sedaghat AR, Kieffer T, Brennan T, Lee PK, Wind-Rotolo M, Haggerty CM, Kamireddi AR, Liu Y, Lee J, Persaud D, Gallant JE, Cofrancesco J, Quinn TC, Wilke CO, Ray SC, Siliciano JD, Nettles RE, Siliciano RF (2006). "Residual Human Immunodeficiency Virus Type 1 Viremia in Some Patients on Antiretroviral Therapy Is Dominated by a Small Number of Invariant Clones Rarely Found in Circulating CD4+ T Cells‚Ć". J Virol. 80 (13): 6441–6457. doi:10.1128/JVI.00591-06. PMC 1488985Freely accessible. PMID 16775332. 
  2. ^ Calis JC, Rotteveel HP, van der Kuyl AC, Zorgdrager F, Kachala D, van Hensbroek MB, Cornelissen M (2008). "Severe anaemia is not associated with HIV-1 env gene characteristics in Malawian children". BMC Infect Dis. 8: 26. doi:10.1186/1471-2334-8-26. PMC 2311312Freely accessible. PMID 18312662.  open access publication – free to read
  3. ^ Mild M, Esbjörnsson J, Fenyö EM, Medstrand P (2007). "Frequent Intrapatient Recombination between Human Immunodeficiency Virus Type 1 R5 and X4 Envelopes: Implications for Coreceptor Switch‚ñø". J Virol. 81 (7): 3369–3376. doi:10.1128/JVI.01295-06. PMC 1866041Freely accessible. PMID 17251288. 
  4. ^ Pendley CJ, Becker EA, Karl JA, Blasky AJ, Wiseman RW, Hughes AL, O'Connor SL, O'Connor DH (2008). "MHC class I characterization of Indonesian cynomolgus macaques". Immunogenetics. 60 (7): 339–351. doi:10.1007/s00251-008-0292-4. PMC 2612123Freely accessible. PMID 18504574. 
  5. ^ Behnke A, Bunge J, Barger K, Breiner H, Alla V, Stoeck T (2006). "Microeukaryote Community Patterns along an O2/H2S Gradient in a Supersulfidic Anoxic Fjord (Framvaren, Norway)‚Ć". Appl Environ Microbiol. 72 (5): 3626–3636. doi:10.1128/AEM.72.5.3626-3636.2006. PMC 1472314Freely accessible. PMID 16672511. 
  6. ^ Bart A, van Passel MWJ, van Amsterdam K, van der Ende A (2005). "Direct detection of methylation in genomic DNA". Nucleic Acids Res. 33 (14): e124. doi:10.1093/nar/gni121. PMC 1184226Freely accessible. PMID 16091626. 
  7. ^ Andersson LS, Juras R, Ramsey DT, Eason-Butler J, Ewart S, Cothran G, Lindgren G (2008). "Equine Multiple Congenital Ocular Anomalies maps to a 4.9 megabase interval on horse chromosome 6". BMC Genet. 9: 88. doi:10.1186/1471-2156-9-88. PMC 2653074Freely accessible. PMID 19099555.  open access publication – free to read
  8. ^ Tremblay K, Lemire M, Potvin C, Tremblay A, Hunninghake GM, Raby BA, Hudson TJ, Perez-Iratxeta C, Andrade-Navarro MA, Laprise C (2008). "Genes to Diseases (G2D) Computational Method to Identify Asthma Candidate Genes". PLoS ONE. 3 (8): e2907. doi:10.1371/journal.pone.0002907. PMC 2488373Freely accessible. PMID 18682798.  open access publication – free to read
  9. ^ McCullough BJ, Adams JC, Shilling DJ, Feeney MP, Sie KCY, Tempel BL (2007). "3p-Syndrome Defines a Hearing Loss Locus in 3p25.3". Hear Res. 224 (1-2): 51–60. doi:10.1016/j.heares.2006.11.006. PMC 1995240Freely accessible. PMID 17208398. 
  10. ^ Pignone M, Greth KM, Cooper J, Emerson D, Tang J (2006). "Identification of Mycobacteria by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry". J Clin Microbiol. 44 (6): 1963–1970. doi:10.1128/JCM.01959-05. PMC 1489414Freely accessible. PMID 16757585. 
  11. ^ van Amsterdam K, Bart A, van der Ende A (2005). "A Helicobacter pylori TolC Efflux Pump Confers Resistance to Metronidazole". Antimicrob Agents Chemother. 49 (4): 1477–1482. doi:10.1128/AAC.49.4.1477-1482.2005. PMC 1068630Freely accessible. PMID 15793129. 
  12. ^ Baxter SW, Papa R, Chamberlain N, Humphray SJ, Joron M, Morrison C, Ffrench-Constant RH, McMillan WO, Jiggins CD (2008). "Convergent Evolution in the Genetic Basis of Müllerian Mimicry in Heliconius Butterflies". Genetics. 180 (3): 1567–1577. doi:10.1534/genetics.107.082982. PMC 2581958Freely accessible. PMID 18791259. 
  13. ^ Siddall ME, Trontelj P, Utevsky SY, Nkamany M, Macdonald KS (2007). "Diverse molecular data demonstrate that commercially available medicinal leeches are not Hirudo medicinalis". Proc Biol Sci. 274 (1617): 1481–1487. doi:10.1098/rspb.2007.0248. PMC 2176162Freely accessible. PMID 17426015. 
  14. ^ Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V, Epstein S (2007). "Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?". PLoS ONE. 2 (8): e728. doi:10.1371/journal.pone.0000728. PMC 1940325Freely accessible. PMID 17710128.  open access publication – free to read

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