# CodonCode Aligner

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DNA sequence software

CodonCode Aligner Developer CodonCode Corporation Stable release 12.0.1 / 2024 Operating system Mac OS X, Windows Type Bioinformatics License commercial; free for limited use (trace viewing & editing) Website http://www.codoncode.com/aligner

**CodonCode Aligner** is a commercial application for DNA [sequence assembly](/source/Sequence_assembly), [sequence alignment](/source/Sequence_alignment), and editing on [Mac OS X](/source/Mac_OS_X) and [Windows](/source/Microsoft_Windows).

## Features

Features include [chromatogram](/source/Chromatogram) editing, end clipping, and vector trimming, [sequence assembly](/source/Sequence_assembly) and contig editing, aligning [cDNA](/source/CDNA) against genomic templates, [sequence alignment](/source/Sequence_alignment) and editing, alignment of contigs to each other with [ClustalW](/source/ClustalW), [MUSCLE](/source/Multiple_Sequence_Comparison_by_Log-Expectation), or built-in algorithms, mutation detection, including detection of heterozygous [single-nucleotide polymorphism](/source/Single-nucleotide_polymorphism), analysis of heterozygous insertions and deletions, start online [BLAST](/source/BLAST_(biotechnology)) 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](/source/Phred_base_calling), [Phrap](/source/Phrap), [ClustalW](/source/ClustalW), and [MUSCLE](/source/MUSCLE_(alignment_software)).

## 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

- [Phred base calling](/source/Phred_base_calling)

- [Phrap](/source/Phrap)

- [Consed](/source/Consed)

## References

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1. **[^](#cite_ref-Calis2008th_2-0)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2311312). *BMC Infect Dis*. **8**: 26. [doi](/source/Doi_(identifier)):[10.1186/1471-2334-8-26](https://doi.org/10.1186%2F1471-2334-8-26). [PMC](/source/PMC_(identifier)) [2311312](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2311312). [PMID](/source/PMID_(identifier)) [18312662](https://pubmed.ncbi.nlm.nih.gov/18312662).

1. **[^](#cite_ref-Mild2007ec_3-0)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866041). *J Virol*. **81** (7): 3369–3376. [doi](/source/Doi_(identifier)):[10.1128/JVI.01295-06](https://doi.org/10.1128%2FJVI.01295-06). [PMC](/source/PMC_(identifier)) [1866041](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866041). [PMID](/source/PMID_(identifier)) [17251288](https://pubmed.ncbi.nlm.nih.gov/17251288).

1. **[^](#cite_ref-Pendley2008xq_4-0)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612123). *Immunogenetics*. **60** (7): 339–351. [doi](/source/Doi_(identifier)):[10.1007/s00251-008-0292-4](https://doi.org/10.1007%2Fs00251-008-0292-4). [PMC](/source/PMC_(identifier)) [2612123](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612123). [PMID](/source/PMID_(identifier)) [18504574](https://pubmed.ncbi.nlm.nih.gov/18504574).

1. **[^](#cite_ref-Behnke2006eu_5-0)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1472314). *Appl Environ Microbiol*. **72** (5): 3626–3636. [doi](/source/Doi_(identifier)):[10.1128/AEM.72.5.3626-3636.2006](https://doi.org/10.1128%2FAEM.72.5.3626-3636.2006). [PMC](/source/PMC_(identifier)) [1472314](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1472314). [PMID](/source/PMID_(identifier)) [16672511](https://pubmed.ncbi.nlm.nih.gov/16672511).

1. **[^](#cite_ref-Bart2005fc_6-0)** Bart A, van Passel MWJ, van Amsterdam K, van der Ende A (2005). ["Direct detection of methylation in genomic DNA"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1184226). *Nucleic Acids Res*. **33** (14): e124. [doi](/source/Doi_(identifier)):[10.1093/nar/gni121](https://doi.org/10.1093%2Fnar%2Fgni121). [PMC](/source/PMC_(identifier)) [1184226](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1184226). [PMID](/source/PMID_(identifier)) [16091626](https://pubmed.ncbi.nlm.nih.gov/16091626).

1. **[^](#cite_ref-Andersson2008qo_7-0)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653074). *BMC Genet*. **9**: 88. [doi](/source/Doi_(identifier)):[10.1186/1471-2156-9-88](https://doi.org/10.1186%2F1471-2156-9-88). [PMC](/source/PMC_(identifier)) [2653074](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653074). [PMID](/source/PMID_(identifier)) [19099555](https://pubmed.ncbi.nlm.nih.gov/19099555).

1. **[^](#cite_ref-Tremblay2008kl_8-0)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2488373). *PLOS ONE*. **3** (8) e2907. [Bibcode](/source/Bibcode_(identifier)):[2008PLoSO...3.2907T](https://ui.adsabs.harvard.edu/abs/2008PLoSO...3.2907T). [doi](/source/Doi_(identifier)):[10.1371/journal.pone.0002907](https://doi.org/10.1371%2Fjournal.pone.0002907). [PMC](/source/PMC_(identifier)) [2488373](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2488373). [PMID](/source/PMID_(identifier)) [18682798](https://pubmed.ncbi.nlm.nih.gov/18682798).

1. **[^](#cite_ref-McCullough2007pi_9-0)** McCullough BJ, Adams JC, Shilling DJ, Feeney MP, Sie KCY, Tempel BL (2007). ["3p-Syndrome Defines a Hearing Loss Locus in 3p25.3"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1995240). *Hear Res*. **224** (1–2): 51–60. [doi](/source/Doi_(identifier)):[10.1016/j.heares.2006.11.006](https://doi.org/10.1016%2Fj.heares.2006.11.006). [PMC](/source/PMC_(identifier)) [1995240](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1995240). [PMID](/source/PMID_(identifier)) [17208398](https://pubmed.ncbi.nlm.nih.gov/17208398).

1. **[^](#cite_ref-Pignone2006hq_10-0)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1489414). *J Clin Microbiol*. **44** (6): 1963–1970. [doi](/source/Doi_(identifier)):[10.1128/JCM.01959-05](https://doi.org/10.1128%2FJCM.01959-05). [PMC](/source/PMC_(identifier)) [1489414](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1489414). [PMID](/source/PMID_(identifier)) [16757585](https://pubmed.ncbi.nlm.nih.gov/16757585).

1. **[^](#cite_ref-Amsterdam2005dw_11-0)** van Amsterdam K, Bart A, van der Ende A (2005). ["A Helicobacter pylori TolC Efflux Pump Confers Resistance to Metronidazole"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1068630). *Antimicrob Agents Chemother*. **49** (4): 1477–1482. [doi](/source/Doi_(identifier)):[10.1128/AAC.49.4.1477-1482.2005](https://doi.org/10.1128%2FAAC.49.4.1477-1482.2005). [PMC](/source/PMC_(identifier)) [1068630](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1068630). [PMID](/source/PMID_(identifier)) [15793129](https://pubmed.ncbi.nlm.nih.gov/15793129).

1. **[^](#cite_ref-Baxter2008mb_12-0)** 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"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581958). *Genetics*. **180** (3): 1567–1577. [doi](/source/Doi_(identifier)):[10.1534/genetics.107.082982](https://doi.org/10.1534%2Fgenetics.107.082982). [PMC](/source/PMC_(identifier)) [2581958](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581958). [PMID](/source/PMID_(identifier)) [18791259](https://pubmed.ncbi.nlm.nih.gov/18791259).

1. **[^](#cite_ref-Siddall2007cr_13-0)** Siddall ME, Trontelj P, Utevsky SY, Nkamany M, Macdonald KS (2007). ["Diverse molecular data demonstrate that commercially available medicinal leeches are not Hirudo medicinalis"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176162). *Proc Biol Sci*. **274** (1617): 1481–1487. [doi](/source/Doi_(identifier)):[10.1098/rspb.2007.0248](https://doi.org/10.1098%2Frspb.2007.0248). [PMC](/source/PMC_(identifier)) [2176162](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176162). [PMID](/source/PMID_(identifier)) [17426015](https://pubmed.ncbi.nlm.nih.gov/17426015).

1. **[^](#cite_ref-Stoeck2007xr_14-0)** 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?"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1940325). *PLOS ONE*. **2** (8) e728. [Bibcode](/source/Bibcode_(identifier)):[2007PLoSO...2..728S](https://ui.adsabs.harvard.edu/abs/2007PLoSO...2..728S). [doi](/source/Doi_(identifier)):[10.1371/journal.pone.0000728](https://doi.org/10.1371%2Fjournal.pone.0000728). [PMC](/source/PMC_(identifier)) [1940325](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1940325). [PMID](/source/PMID_(identifier)) [17710128](https://pubmed.ncbi.nlm.nih.gov/17710128).

## External links

- [CodonCode Aligner homepage](http://www.codoncode.com/aligner)

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Adapted from the Wikipedia article [CodonCode Aligner](https://en.wikipedia.org/wiki/CodonCode_Aligner) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/CodonCode_Aligner?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.