View source for CodonCode Aligner

{{Short description|DNA sequence software}}
{{Infobox software
| name = CodonCode Aligner
| logo = 
| screenshot = 
| caption = 
| developer = CodonCode Corporation
| latest release version = 12.0.1
| latest release date = 2024
| latest preview version = 
| latest preview date = 
| 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 [[Microsoft Windows|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]], [[Multiple Sequence Comparison by Log-Expectation|MUSCLE]], or built-in algorithms, mutation detection, including detection of heterozygous [[single-nucleotide polymorphism]], analysis of heterozygous insertions and deletions, start online [[BLAST (biotechnology)|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 base calling|Phred]], [[Phrap]], [[ClustalW]], and [[MUSCLE (alignment software)|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,<ref name="Bailey2006rq">{{cite journal |vauthors=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|year=2006|title=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†.|journal=J Virol|volume=80|pages=6441–6457 |pmid=16775332 |issue=13 |doi=10.1128/JVI.00591-06 |pmc=1488985}}</ref><ref name="Calis2008th">{{cite journal |vauthors=Calis JC, Rotteveel HP, van der Kuyl AC, Zorgdrager F, Kachala D, van Hensbroek MB, Cornelissen M|year=2008|title=Severe anaemia is not associated with HIV-1 env gene characteristics in Malawian children.|journal=BMC Infect Dis|volume=8|page=26 |pmid=18312662 |doi=10.1186/1471-2334-8-26 |pmc=2311312 |doi-access=free }} {{open access}}</ref><ref name="Mild2007ec">{{cite journal |vauthors=Mild M, Esbjörnsson J, Fenyö EM, Medstrand P|year=2007|title=Frequent Intrapatient Recombination between Human Immunodeficiency Virus Type 1 R5 and X4 Envelopes: Implications for Coreceptor Switch'ñø.|journal=J Virol|volume=81|pages=3369–3376 |pmid=17251288 |issue=7 |doi=10.1128/JVI.01295-06 |pmc=1866041}}</ref> biogeography and environmental biology,<ref name="Pendley2008xq">{{cite journal |vauthors=Pendley CJ, Becker EA, Karl JA, Blasky AJ, Wiseman RW, Hughes AL, O'Connor SL, O'Connor DH|year=2008|title=MHC class I characterization of Indonesian cynomolgus macaques.|journal=Immunogenetics|volume=60|pages=339–351 |pmid=18504574 |issue=7 |doi=10.1007/s00251-008-0292-4 |pmc=2612123}}</ref><ref name="Behnke2006eu">{{cite journal |vauthors=Behnke A, Bunge J, Barger K, Breiner H, Alla V, Stoeck T|year=2006|title=Microeukaryote Community Patterns along an O2/H2S Gradient in a Supersulfidic Anoxic Fjord (Framvaren, Norway)'Ä†.|journal=Appl Environ Microbiol|volume=72|pages=3626–3636 |pmid=16672511 |issue=5 |doi=10.1128/AEM.72.5.3626-3636.2006 |pmc=1472314}}</ref> DNA methylation studies,<ref name="Bart2005fc">{{cite journal |vauthors=Bart A, ((van Passel MWJ)), van Amsterdam K, van der Ende A|year=2005|title=Direct detection of methylation in genomic DNA.|journal=Nucleic Acids Res|volume=33|pages=e124 |pmid=16091626 |issue=14 |doi=10.1093/nar/gni121 |pmc=1184226}}</ref> genetic diseases,<ref name="Andersson2008qo">{{cite journal |vauthors=Andersson LS, Juras R, Ramsey DT, Eason-Butler J, Ewart S, Cothran G, Lindgren G|year=2008|title=Equine Multiple Congenital Ocular Anomalies maps to a 4.9 megabase interval on horse chromosome 6.|journal=BMC Genet|volume=9|page=88 |pmid=19099555 |doi=10.1186/1471-2156-9-88 |pmc=2653074 |doi-access=free }} {{open access}}</ref><ref name="Tremblay2008kl">{{cite journal |vauthors=Tremblay K, Lemire M, Potvin C, Tremblay A, Hunninghake GM, Raby BA, Hudson TJ, Perez-Iratxeta C, Andrade-Navarro MA, Laprise C|year=2008|title=Genes to Diseases (G2D) Computational Method to Identify Asthma Candidate Genes.|journal=PLOS ONE|volume=3|doi=10.1371/journal.pone.0002907|pmid=18682798|issue=8|pmc=2488373|article-number=e2907|bibcode=2008PLoSO...3.2907T|doi-access=free}} {{open access}}</ref><ref name="McCullough2007pi">{{cite journal |vauthors=McCullough BJ, Adams JC, Shilling DJ, Feeney MP, ((Sie KCY)), Tempel BL|year=2007|title=3p-Syndrome Defines a Hearing Loss Locus in 3p25.3.|journal=Hear Res|volume=224|pages=51–60 |pmid=17208398 |issue=1–2 |doi=10.1016/j.heares.2006.11.006 |pmc=1995240}}</ref> clinical microbiology,<ref name="Pignone2006hq">{{cite journal |vauthors=Pignone M, Greth KM, Cooper J, Emerson D, Tang J|year=2006|title=Identification of Mycobacteria by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry.|journal=J Clin Microbiol|volume=44|pages=1963–1970 |pmid=16757585 |issue=6 |doi=10.1128/JCM.01959-05 |pmc=1489414}}</ref><ref name="Amsterdam2005dw">{{cite journal |vauthors=van Amsterdam K, Bart A, van der Ende A|year=2005|title=A Helicobacter pylori TolC Efflux Pump Confers Resistance to Metronidazole.|journal=Antimicrob Agents Chemother|volume=49|pages=1477–1482 |pmid=15793129 |issue=4 |doi=10.1128/AAC.49.4.1477-1482.2005 |pmc=1068630}}</ref> and evolution research and phylogenetics.<ref name="Baxter2008mb">{{cite journal |vauthors=Baxter SW, Papa R, Chamberlain N, Humphray SJ, Joron M, Morrison C, Ffrench-Constant RH, McMillan WO, Jiggins CD|year=2008|title=Convergent Evolution in the Genetic Basis of Müllerian Mimicry in Heliconius Butterflies.|journal=Genetics|volume=180|pages=1567–1577 |pmid=18791259 |issue=3 |doi=10.1534/genetics.107.082982 |pmc=2581958}}</ref><ref name="Siddall2007cr">{{cite journal |doi=10.1098/rspb.2007.0248 |vauthors=Siddall ME, Trontelj P, Utevsky SY, Nkamany M, Macdonald KS|year=2007|title=Diverse molecular data demonstrate that commercially available medicinal leeches are not Hirudo medicinalis.|journal=Proc Biol Sci|volume=274 |issue=1617|pages=1481–1487 |pmid=17426015 |pmc=2176162}}</ref><ref name="Stoeck2007xr">{{cite journal |vauthors=Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V, Epstein S|year=2007|title=Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?|journal=PLOS ONE|volume=2 |pmid= 17710128 | doi = 10.1371/journal.pone.0000728 |issue=8 |pmc=1940325 |article-number=e728|bibcode=2007PLoSO...2..728S|doi-access=free}} {{open access}}</ref>

== See also ==
*[[Phred base calling]]
*[[Phrap]]
*[[Consed]]

== References ==
{{reflist}}

== External links ==
*[http://www.codoncode.com/aligner CodonCode Aligner homepage]

[[Category:Bioinformatics software]]
[[Category:Computational science]]