CodonCode Aligner

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DNA sequence software

title: "CodonCode Aligner" type: doc version: 1 created: 2026-02-28 author: "Wikipedia contributors" status: active scope: public tags: ["bioinformatics-software", "computational-science"] description: "DNA sequence software" topic_path: "technology/computing" source: "https://en.wikipedia.org/wiki/CodonCode_Aligner" license: "CC BY-SA 4.0" wikipedia_page_id: 0 wikipedia_revision_id: 0

::summary DNA sequence software ::

::data[format=table title="Infobox software"]

Field	Value
name	CodonCode Aligner
developer	CodonCode Corporation
latest release version	12.0.1
latest release date	2024
operating system	Mac OS X, Windows
genre	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, 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, biogeography and environmental biology, DNA methylation studies, genetic diseases, clinical microbiology, and evolution research and phylogenetics.

References

(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'Ä†.". J Virol.
(2008). "Severe anaemia is not associated with HIV-1 env gene characteristics in Malawian children.". BMC Infect Dis.
(2007). "Frequent Intrapatient Recombination between Human Immunodeficiency Virus Type 1 R5 and X4 Envelopes: Implications for Coreceptor Switch'ñø.". J Virol.
(2008). "MHC class I characterization of Indonesian cynomolgus macaques.". Immunogenetics.
(2006). "Microeukaryote Community Patterns along an O2/H2S Gradient in a Supersulfidic Anoxic Fjord (Framvaren, Norway)'Ä†.". Appl Environ Microbiol.
(2005). "Direct detection of methylation in genomic DNA.". Nucleic Acids Res.
(2008). "Equine Multiple Congenital Ocular Anomalies maps to a 4.9 megabase interval on horse chromosome 6.". BMC Genet.
(2008). "Genes to Diseases (G2D) Computational Method to Identify Asthma Candidate Genes.". PLOS ONE.
(2007). "3p-Syndrome Defines a Hearing Loss Locus in 3p25.3.". Hear Res.
(2006). "Identification of Mycobacteria by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry.". J Clin Microbiol.
(2005). "A Helicobacter pylori TolC Efflux Pump Confers Resistance to Metronidazole.". Antimicrob Agents Chemother.
(2008). "Convergent Evolution in the Genetic Basis of Müllerian Mimicry in Heliconius Butterflies.". Genetics.
(2007). "Diverse molecular data demonstrate that commercially available medicinal leeches are not Hirudo medicinalis.". Proc Biol Sci.
(2007). "Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?". PLOS ONE.

::callout[type=info title="Wikipedia Source"] This article was imported from Wikipedia and is available under the Creative Commons Attribution-ShareAlike 4.0 License. Content has been adapted to SurfDoc format. Original contributors can be found on the article history page. ::