CodonCode Aligner

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

CodonCode Aligner
CodonCode Aligner
DeveloperCodonCode Corporation
Stable release
12.0.1 / 2024
Operating systemMac OS X, Windows
TypeBioinformatics
Licensecommercial; free for limited use (trace viewing & editing)
Websitehttp://www.codoncode.com/aligner

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

Features

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), RFLP analysis, virtual cloning, including Gibson Assembly, restriction cloning, and TA and TOPO cloning, primer design, phylogenetic trees, difference tables, trace sharpening, and support for Phred, Phrap, ClustalW, and MUSCLE.

History

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, 2006, 2007, 2009, 2010, 2012, 2013, 2014, 2015, 2017, 2018, 2019, 2021, 2023, and 2024.

In April 2009, CodonCode Aligner had been cited in more than 400 scientific publications. In 2025 CodonCode Aligner has been cited in thousands of peer-reviewed 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

References

  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 1488985. 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 2311312. PMID 18312662. Open access icon
  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 1866041. 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 2612123. 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 1472314. 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 1184226. 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 2653074. PMID 19099555. Open access icon
  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. Bibcode:2008PLoSO...3.2907T. doi:10.1371/journal.pone.0002907. PMC 2488373. PMID 18682798. Open access icon
  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 1995240. 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 1489414. 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 1068630. 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 2581958. 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 2176162. 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. Bibcode:2007PLoSO...2..728S. doi:10.1371/journal.pone.0000728. PMC 1940325. PMID 17710128. Open access icon

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