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 (the email address has to be from your university or non-profit research institution)
  • 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
    .
  • Dr. Janske van de Crommenacker, Seychelles Islands Foundation, Republic of Seychelles
    Janske works for the Seychelles Islands Foundation, a public trust that manages and protects the UNESCO World Heritage Site of the Aldabra Atoll. Her current project aims to study the taxonomic status of two local landbird species: the Aldabra fody and the Aldabra rail. Futhermore she is investigating the extent of the influence through an invasive fodies species that is likely to hybridize with the endemic Aldabra fodies, possibly causing their extinction.
    Learn more about conservation on the Aldabra Atoll in Janske's user showcase.
  • Dr. Carmen Tamariz Angeles, Universidad Nacional Santiago Antúnez de Mayolo, Peru
    Carmen is deeply involved in barcoding and molecular genetic identification from Peruvian microorganisms and plants. Her research laboratoy at the Universidad Nacional Santiago Antúnez de Mayolo is focused on studying bioremedation, bioactive compounds, enzyme production and plant-growth promotion of plants and microorganisms found in the high Andes.
    Read about these biotechnological applications in Carmen's user showcase.
  • Dr. Elena Kravchenko, Joint Institute for Nuclear Research, Russia
    Dr. Kravchenko researches the biological effect of ionizing radiations. At the Radiation and Molecular Genetics Group (JINR), she conducts studies on the molecular-genetic analysis of gamma and neutron induced mutations for a number of Drosophila melanogaster genes after irradiation of generative cells. Of specific interest are the relative activity of different repair systems in generative and somatic cells of eukaryotes after radiation damage, to estimate the number and type of mutations caused by different types of radiation, and to determine the spectrum of inherited changes in DNA caused by the studied types of radiation. Dr. Kravchenko and her colleagues use CodonCode Aligner to build contigs and reconstruct the regulatory and structural parts of different mutant genes, and to then compare the resulting gene sequence with the consensus sequence and other mutant sequences.
  • Dr. Marc Eléaume, Museum national d’Histoire naturelle, France
    Dr. Eléaume's research at the Département Systématique & Evolution in MNH focuses on the taxonomy and evolution of crinoids. Molecular approaches in his studies help to understand the species delimitations within genera or species complexes. He uses traditional sanger sequencing as well as NGS sequencing to identify and find new molecular markers, and to develop SNP essays to distinguish crinoid species.
  • Dr. Szun Tay, The University of New South Wales, EMBL Australia
    Szun is currently interested in T cell immunity to cancer and infection and studies how killer T cells migrate and behave when they encounter tumours. In her research at the EMBL Australia, she uses CodonCode Aligner for all standard molecular cloning steps, to quick-find restriction sites, to analyse sequenced reactions, and for sequence assembly. She also uses Aligner to design novel peptides and proteins and for querying microRNA and gRNA target sequences, as well as for analyzing indels.
  • Dr. David Bean, Federation University Australia
    David's research at the Federation University Australia is focused on antibiotic resistance in pathogenic bacteria. He is interested in epidemiology, resistance mechanisms and novel treatment of resistant organisms. David uses CodonCode Aligner to analyze DNA sequences of bacterial pathogens to identify mutations in genes which may lead to resistance to antibiotics.
  • Carlos Alonso Maya Lastra, Instituto de Ecología, A.C, México
    Carlos Alonso Maya Lastra is a taxonomist examining the phylogenetic relationships in some genera of the Euphorbiaceae family. He currently studies the American endemic genus Cnidoscolus, exploring its biogeographical patterns and phylogeny at the Institute of Ecology, A.C. in Mexico. He uses CodonCode Aligner to clip, assemble and analyze the sequences for differences.
  • Dr. Oliver Balmer, Swiss Tropical and Public Health Institute, Switzerland
    Dr. Balmer is part of a research group at the Swiss Tropical and Public Health Institute that works on various zoonotic diseases. He studies the ecology and evolution of diverse zoonotic parasites such as Trypanosoma brucei (causing human African sleeping sicknes) and trematodes (causing schistosomiasis and fascioliasis). Dr. Balmer: "Our most urgent need is to develop and optimize PCR approaches to type and sequence under-studied parasites from remote places. CCA's power for looking at multiple sequence trace files together and analyze variation between species and genotypes during marker development is the key reason why I would be eager to use it."
  • Ines Badano, Universidad Nacional de Misiones, Argentina
    In her lab, Ines and her co-researchers use Human Papillomavirus genome sequences as a novel way to examine the evolution and migratory patterns of the human population of Misiones (Argentina, South America). Their current research involves the analysis of two genetic markers: HPV16 sequences and mitochondrial DNA within Misiones population. The combination of mtDNA data and data on viral sequences is providing them with new insights into the genetic history of Misiones and helps to trace the source of specific disease outbreaks. CodonCode Aligner is used to align, edit and BLAST-search hundreds of samplesfor phylogenetic analysis.
  • Marc Delêtre, National University of Ireland Galway, Ireland
    Marc's research is focused on farmer-plant interactions and their genetic and evolutionary consequences for crop plants. Currently, he has been working the social dynamics of crop pandemics as part of his ongoing research at the Plant and Agricultural Biosciences Centre, National University of Ireland Galway. Marc compares anthropological, genetic, and plant epidemiological data to explore how the interplay of social structures and local/regional networks of seed exchange influences the dynamics of plant pathogen epidemics. For this purpose, he has been investigating the effects of local networks of seed exchange on spatial patterns of genetic variation in the African Cassava Mosaic Virus (ACMV). He uses CodonCode to assemble and align DNA regions of the virus to analyze geographic patterns of genetic variation across viral meta-populations.
  • Dr Jon Wetton, University of Leicester, UK
    Dr. Jon Wetton's research focuses on the development of novel genetic markers for population studies. These markers have a wide range of appliactions like the development of minisatellite profiling tests that can be used to identify the parentage of birds of prey, which, for example, allows to prove theft of wild nestlings. Another application is the identification of illegally traded items derived from endangered species, such as tiger bone in traditional East Asian medicines. Dr. Wetton and his collaborators also used mitochondrial profiles to help determine the origin of animal hairs that were recovered during the investigation of serious human crime. He is currently creating a database with mitochondrial varaitions of dog and cat hair samples that can be used to solve these crimes. Furthermore Dr. Wetton is working on the development of primers for monotoring wild animal populations through hair and feacal samples. CodonCode Aligner is used to assemble and compare mitochondrial animal DNA to help with his research.
  • Eunsun Kim, University of Pennsylvania, USA
    Eunsun Kim studiesHepatocellular carcinoma (HCC) at the University of Pennsylvania. More specifically Eunsun and his lab look into the epigenetic mechanisms that drive tumor initiation and progression upon loss of major tumor suppressor genes such as the Rb genes family. Their ultimate goal is to demonstrate that the activation of specific pathways provides survival advantages to HCC cells, and to highlight them as valuable therapeutic targets for HCC treatment. CodonCode Aligner will be used during cloning experiments to analyze vector and gene insertions, to design primers, and to assemble and analyze the construct sequences.
  • João Paulo da Silva Medeiros, MARE - University of Lisbon, Portugal
    João Paulo's PhD research in benthic communities, biotic indices and DNA barcoding takes place at the Marine and Environmental Sciences Centre and at The Southern California Coastal Water Research Project. He focuses his work on low salinity areas (upper areas of estuaries) regarding the assessment of its ecological quality status (EQS) using benthic communities, using both morphological and genetic approaches, in order to, in a near future, develop a tool able to assess EQS of this particular ecosystems.
  • Camille Moreau, Université Libre de Bruxelles, Belgium
    Camille's current research project at the ULB-BIOMAR is focusing on Asteroidea biogeography and phylogeography in the Antarctic. The project is part of the vERSO program. The aim of the project is to complete the knowledge on biodiversity of austral asteroids and to take part in the ecoregionalisation of this large ecosystem. CodonCode Aligner will help Camille to align CO1 sequences from Asteroidea and to verify differences in the sequences.
  • Dr. Mark Chee, Duke University, NC, USA
    Dr. Chee currently works with large broods of Drosophila simulans vinegar/fruit flies as well as Drosophila melanogaster that are used to teach lab courses and to conduct research at Duke University. One of his current interests is the isolation and identification of microorganisms that cause persistent, chronic infection of Drosophila laboratory cultures. CodonCode Aligner will be used to identify these microorganisms, as well as to analyze the sequences of genetic loci in different D. simulans strains.
  • Jonathan Herlet, Technical University Munich, Germany
    Jonathan's field of study at the Technical University of Munich focuses on trying to find ways to produce current and new chemicals from biogenic resources, where the goal is to establish a new „green“ chemistry not depended on fossil resources. His research in this field is the modification and characterization of microbial exopolysaccharides (EPS) synthesis in Pseudomonas species wild types. Examples for currently used EPS are gellan in the food industry or xanthan as a hydrocolloid. He uses CodonCode Aligner to analyze the sequnces of the plasmids and gene knockouts used in the characterization of newly found EPS.
  • Park Chan-Ho, Sunchon National University, Korea
    Park studies the rapid formation of biological soil crust with use of desert lichen and cyanobacteria at the Sunchon National University. Biological soil crusts are considered as a solution to restore degraded desert soil with positive effects on ecosystems, but have a very long recovery time. Park therefore studies the fast induction of biological soil crusts. CodonCode Aligner helps him to align and identify different cyanobacteria, fungi and lichen which he collects as part of his research.
  • Ramanan Devaraj, Academia Sinica, Taiwan
    Ramanan is a PhD student in the Institute of Molecular Biology at Academia Sinica in Taiwan. His reasearch looks at mitochondrial genome varaiations that are connected to Non-Syndromic Hearing Loss in the North Indian Population. CodonCode Aligner is used to align the mitochondrial genome of patients to a reference sequence and identify the mutations.
  • Inęs Carvalho, Instituto Gulbenkian de Ciência, Portugal
    Inês is involved in a conservation project of a very small and endangered resident population of bottlenose dolphins (Tursiops truncatus). She works with the Population and Conservation Genetics Group laboratory at the Instituto Gulbenkian de Cięncia to analyze the molecular data for this project which will be used to address fundamental questions regarding the population structure of resident and non-resident populations of bottlenose dolphins along the Iberian Peninsula.

  • Nathalie Kin, University of Caen Lower Normandy, France
    Nathalie studies the molecular characterization of coronaviruses during her PhD research at the University of Caen. In particular she looks at the evolution of these viruses to understand the phenomena of interspecies jumping. With CodonCode Aligner, Nathalie will assemble the viral sequencing data that will be used for phylogenetic analysis.
  • Amy MacLeod, University of Bielefeld, Germany
    Amy is a PhD student in the Department of Animal Behaviour at the University of Bielefeld. She is working on population genetics, taxonomy, diet and enteric specialisation of marine iguanas on San Cristóbal Island. CodonCode Aligner will help Amy to assemble mitochondrial sequence data which will be used to assess the taxonomic standing of various island populations of marine iguanas.
  • Marta Massana Roselló, University of Barcelona, Spain
    Marta's PhD research in evolutionary ecology combines demographic, morphometric and genetic analysis of the Herman’s tortoise(Testudo hermanni) from Menorca Island. At the Ecology Department of the University of Barcelona, she will use CodonCode Aligner to align mitochondrial sequences in order to find the origins of the populations they located.
  • Dr. Charles Masembe, Makerere University, Uganda
    Dr. Masembe is a veterinarian and molecular geneticist. His research at the Makerere University focuses ongenetically characterizing major animal epidemics with particular emphasis on foot-and-mouth disease and African swine fever in the East African region, and is aimed at unraveling livestock-wildlife disease interactions to design efficient disease control strategies to ensure food security.
  • Dr. Paul Stapp, California State University Fullerton, CA, USA
    Dr. Stapp is a wildlife ecologist in the Department of Biological Sciences at California State University Fullerton. His lab uses molecular techniques to discern movements and population genetic structure of small mammals and to identify source of blood meals of ectoparasites such as fleas. In a current project, he and his students used CodonCode Aligner to align microsatellite sequences for a population genetics study of grasshopper mice, a possible reservoir for plague in North American grasslands, and to try to identify a species of parasitic fly using mitochondrial markers.
  • 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.
  • Balázs Tánczos, Szent Istvan University, Hungary
    Balázs studies vectors and vector-borne pathogens at the Department of Parasitology and Zoology at the Faculty of Veterinary Scienc at the Szent István University. His main project is currently the prevalence of canine leishmaniasis and the vector sandfly species that transmit Leishmania infantum in Hungary. In the frame of these studies he uses CodonCode Aligner to compare sequences of parasites and analyze their phylogeny .
  • Cherise Hedlin, University of Saskatchewan, Canada
    Cherise is working with Dr. Peter Hull, a dermatologist and medical researcher at University of Saskatchewan. They study the genetic mechanisms of various skin diseases in human DNA and use CodonCode Aligner to detect indels and split them into their two separate alleles.
  • Dr. Gang Chen, Graduate School of Oceanography, University of Rhode Island, USA
    At the Graduate School of Oceanography Dr. Chen's research is mainly focused on genetic diversity of marine planktons, particularly the two most diverse groups, copepods and diatoms. In this context he uses CodonCode Aligner for gene-to-genome assembly, mutation detection and analysis, and restriction mapping.
  • Dr. Ashok Pillai, Amrita Institute of Medical Sciences and Research Centre, India
    His lab at the Amrita Institute of Medical Sciences tries to understand the underlying genetic cause of phakomatoses disorders and it’s correlation with the phenotypic manifestations. They use CodonCode Aligner to align their data to a reference sequence, to find heterozygous point mutations and gene deletions, to start Blast searches and to identify amino acid changes caused by mutations.
  • Susana Vazquez, University of Buenos Aires, Argentina
    Susana's researchat the University of Buenos Aires focuses on the study of the structure and function of microbial communities, mainly in hydrocarbon-contaminated Antarctic environments. She uses CodonCode Aligner to assemble reads from both sides of 16S rDNA gene sequences to analyze bacterial communities or isolates.
  • Dr. Bartlomiej Marcin Budny, Poznan University of Medical Sciences, Poland
    Dr. Budny conducts research on congenital defects of the endocrine gland at the Poznan University of Medical Sciences. He researches the molecular pathways of very rare endocrine gland disorders and uses CodonCode Aligner to find and identify novel genetic factors/alterations that are responsible for etiopathogenesis of endocrine gland disorders in humans.
  • Djogbénou Luc, University of Abomey-Calavi, Republic of Benin (West Africa)
    Djogbénou studies carbamate and organophosphate insecticide resistance in Anopheles gambiae, the main malaria vector in West Africa.
  • Dr. Donovan P. German, University of California, Irvine, USA
    His newly launched lab at the University of California, Irvine has two main research projects. In one of their projects they look at the possible positive selection on specific alleles and copy number variation of amylase genes in herbivores using fishes in the family Stichaeidae. The other main research project focuses on the question "What genes control plasticity of digestive tract structure and function?", which they study using the model organism Danio rerio (commonly known as Zebrafish).
  • 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.

 

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