Free Sequence Assembly Software: The CodonCode Aligner License Grant Program

CodonCode Corporation offers free license grants to selected researchers who would like to use CodonCode Aligner in their research, but who do not have funds to purchase a license.

Requirements

To apply for a free license, you must meet the following requirements:

You are employed at a university or non-profit research institution, with an email address at this institution.
You must follow the application instructions below.
You agree not to sell or otherwise transfer the license.

Please note that only a limited number of free licenses is available, and that not all qualifying applicants will receive a free license.

Application Instructions

To apply for a free license for CodonCode Aligner, please submit a detailed application by email to grants (at) codoncode.com.

Please include the following information:

Your full name and email address
Your current place of employment or study
A summary of your education or a resume
A description of your research
An explanation how CodonCode Aligner can help you in your research (for example, what kind of sequence assembly and alignment needs you have as part of your research)
Links to your lab website (if you have one)
An explanation why you are applying for a free license
A statement that you understand that the license, if granted, may not be sold or transfered to others, or used at for-profit institutions

Please make sure to include all the information requested above; applications that are incomplete or extremely short will be ignored.

Before submitting an application, you should of course download the trial version of CodonCode Aligner, and verify that it meets your needs.

License Grant Recipients

Prof. John D. ("Jack") Pettigrew FRS, Queensland Brain Institute, St Lucia, Australia
Prof. Jack Pettigrew FRS from the Queensland Brain Institute researches the biofilm on Bradshaw rock art from Australia. He uses CodonCode Aligner to study the microorganisms found in this biofilm and hopes to use the evoultionary information contained in these microorgansims to date the paintings whose age is currently unkown.
Have a look at Jack's user showcase.
Crista Burke,Tufts University, Medford, MA, USA
PhD student Crista studies different aspects of evolution, speciation and mutation of the European Corn Borer (ECB) at the Dopman Laboratory at Tufts. Her research focuses on the post-diapause development time of the ECB and its connection to the gene flow between populations, as well as the temporal isolation and its link to its genetic locus.
Get more information about her research, in Crista's user showcase.
Muhammad Ashfaq, Ph.D., National Institute for Biotechnology and Genetic Engineering, Pakistan
Muhammad's research group works on barcoding economically important insect species of Pakistan, which is a collaborative project between Muhammad's lab at the National Institute for Biotechnology and Genetic Engineering (NIGBE) and the Biodiversity Institute of Ontario (BIO), Canada.
For more information about this project, look at Muhammad's user showcase.
Michael MacDonald, San José State University, California, USA
Michael studies population genetics and phylogeography of the Greater Roadrunner (Geococcyx californianus). He uses mitochondrial and nuclear markers to assess the genetic variation and gene flow in roadrunners.
Read about Michael's research in his user showcase.
Felippe Lourenço Claro, São Paulo University, Brazil
Felippe's PhD research looks at the dynamics, conservation, distribution and evolution of repetitive DNA elements in fish. He uses CodonCode Aligner to analyze many sequences of the electric knife fish to construct a genomic library of repetitive elements of six different Eigenmannia species.
Look at his user showcase for more details.
Logan Kistler, Pennsylvania State University, University Park, PA, USA
Logan researches the ancient precursors of American food plants at the Newsom Environmental Archaeology Lab and at the Shapiro Molecular Evolution/Ancient DNA Lab. His current projects include analyzing ancient DNA of the prehistoric eastern North American Chenopod (Chenopodium sp.) to determine its domestication, and studying the phylogeography of the bottle gourd (Lagenaria siceraria) and its arrival in the New World.
Learn more about his research in Logan's user showcase.
Dr. Velavan TP, Institute of Tropical Medicine, University of Tübingen, Germany
His research group focuses mainly on infection and immunity. The main research focus is on infectious diseases such as malaria, leprosy, chagas, and hepatitis and helminth parasites. Dr. Velavan TP and his researchers investigate the role of host genetic polymorphisms during disease episodes to enhance the understanding of how complex cellular and molecular mechanisms regulate the host immune response to infections.
Jim T. Padin, Silliman University, Philippines
Jim's research project at the Silliman University Marine Laboratory deals with the phylogeny and population structure of jacks (Osteichthyes: Carangidae) occurring in Taal Lake, Philippines. The said lake was once a marine environment until its connection to the sea was narrowed into a small river several hundred years in the past. Several marine species were trapped in the lake and diverged from their marine relatives. Jim looks at phylogenetic analysis and population structure studies to learn about its relationship with the marine conspecifics and to determine gene flow between freshwater and marine jacks. Future direction of this project will be to come up with a management strategy for a sustainable fishery of jacks in the lake that will protect the correct species and critical ecosystems.
Dr. Robert Sheehy, Radford University, USA
Students in his lab in the Biology Department at the Radford University are currently working on identifying polymorphic microsatellite loci for Northern Spotted Owls (Strix occidentalis) and Barred Owls (Strix varia) for use in studies of introgression which is occurring in the forests of Eastern Washington and Oregon. They will use CodonCode Aligner for the trimming of vector sequences as well as the alignment and generation of consensus sequences from forward and reverse sequencing reactionsthat will facilitate the downstream analysis required for the design of PCR primers required to successfully amplify polymorphic microsatellite loci. In phylogeographic studies, they plan to use the base calling and sequence alignment features of CodonCode Aligner.
Dr. Matthew Pelletier, Houghton College, NY, USA
Dr. Pelletier and some of his undergraduate students at Houghton College are currently working on a project which is aimed at cloning and sequencing a ~3500 bp cDNA that may be involved in insect development. They are trying to generate a full-length cDNA, as well as determine the structure of the gene, in terms of introns and exons. Their ultimate goal will be to express recombinant protein and test for enzymatic activity and produce antibodies for further studies, as well as to attempt RNAi for this gene to determine whether a physiological effect is observed.
James Cohen, Texas A&M International University, USA
His research aims to understand the relationships of Boraginaceae, a plant family that includes over 100 genera and 1,600 species, with members found throughout the world. In order to try to understand these relationships, James utilizes multiple DNA regions from the plastid, mitochondrial, and nuclear genomes to reconstruct phylogenies, and with these phylogenies, he examines morphological and molecular character evolution.
Leonid Kulakov, The Queen’s University of Belfast, Ireland
Leonid's current research is mostly focused on the bacteriophage metagenomics and genomics / genetics of new bacteriophages of Pseudomonas species at the School of Biological Sciences at the Queen’s University of Belfast. He and his research group study the role of bacteriophages in horizontal gene transfer. They also work with novel phages of Pseudomonas aeruginosa and Pseudomonas putida, which has both environmental and clinical significance as P. aeruginosa phages are considered as potential therapeutical agents.
Gabriel Golczer, University Simón Bolívar, Caracas, Venezuela
Gabriel looks at the phylogenetics of sandflies (Lutzomyia), which are a vector of Leishmaniasis, Bartonella and a group of viruses. His goal is to resolve taxonomic problems between the 400 species of the genus Lutzomyia, and to develop molecular markers for fast identification.
David Grand, Cancéropôle Toulouse, France
David works in a clinical molecular diagnostics laboratory at the Hospital Purpan and is also involved in cancer research at Cancéropôle Toulouse. He develops techniques for molecular diagnostics, clonality, Kras, BRAF, JAK2 and microsatellite instability. In addition, David works on the genome database Ensembl and teaches students about DNA sequencing, and sequence manipulation on the computer.
Cobus Meyer Visagie, University of Stellenbosch, South Africa
Cobus studies the taxonomy of Penicillium spp from the Fynbos biome at the laboratory of Dr. Karin Jacobs. He analyzes multiple genes for his phylogenetic comparisons, and uses CodonCode Aligner to assemble the large amount of sequences he has, and edit the resulting contigs.
Charles Budinoff, University of Tennessee, Knoxville, TN, USA
Charles studies viruses that infect marine bacteria as part of his Ph. D. research. He plans to use CodonCode Aligner to assemble and align 16S, ITS, and 23S rDNA genes from several hundred marine bacteria isolates.
Alison McLean, Griffith University, Brisbane, Australia
Alison's Ph. D. research examines the phylogeography of a wide-spread Australian bird. In addition to using CodonCode Aligner for sequence assembly and alignments, Alison uses Aligner's heterozygous indel analysis functions to analyze nuclear sequence data from multiple specimen and loci.
Fan Liu, Xiamen University, China
Fan Liu studies nematode parasitology in the laboratory of Prof. Dr. Tang. Fan "fell in love" with CodonCode Aligner as a visiting scholar in Prof. Steven Nadler's lab at UC Davis.
Alex Compton, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Alex's research examines antiviral gene diversity in Old World Monkeys. In Prof. Dr. Michael Emerman's lab, he studies whether polymorphism in cytidine deaminases genes of African Green Monkeys results in differential antiviral function against HIV-1 replication and retrotranposition events.