The CAOS algorithm is described in the following publications:

  1. Sarkar IN, Thornton JW, Planet PJ, Figurski DH, Schierwater B, and DeSalle R. An Autotmated Phylogenetic Key for Classifying Homoboxes. Molecular Genetics and Evolution (2002) 24: 388-399.
  2. Sarkar IN, Planet PJ, and DeSalle R. CAOS software for use in character-based DNA barcoding. Molecular Ecology Resources (2008) 8, 1256-1259.

CAOS has been used and/or cited by the following publications:

  1. Jakob, W., et al., The Trox-2 Hox/ParaHox gene of Trichoplax (Placozoa) marks an epithelial boundary. Development Genes and Evolution, 2004. 214(4): p. 170-175.
  2. Stadler, P.F., et al., Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii. Molecular Phylogenetics and Evolution, 2004. 32(3): p. 686-694.
  3. Collins, A.G., et al., Phylogenetic context and basal metazoan model systems. Integrative and Comparative Biology, 2005. 45(4): p. 585-594.
  4. DeSalle, R., Animal phylogenomics: Multiple interspecific genome comparisons, in Molecular Evolution: Producing the Biochemical Data, Part B. 2005. p. 104-133.
  5. DeSalle, R., M.G. Egan, and M. Siddall, The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society B-Biological Sciences, 2005. 360(1462): p. 1905-1916.
  6. Chiu, J.C., et al., OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics, 2006. 22(6): p. 699-707.
  7. de la Torre, J.E.B., et al., ESTimating plant phylogeny: lessons from partitioning. Bmc Evolutionary Biology, 2006. 6.
  8. DeSalle, R., What's in a character? Journal of Biomedical Informatics, 2006. 39(1): p. 6-17.
  9. Rubinoff, D., S. Cameron, and K. Will, A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification. Journal of Heredity, 2006. 97(6): p. 581-594.
  10. Kelly, R.P., et al., DNA barcoding using chitons (genus Mopalia). Molecular Ecology Notes, 2007. 7(2): p. 177-183.
  11. Luo, J., et al., PCR survey of Hox genes in the goldfish Carassius auratus auratus. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution, 2007. 308B(3): p. 250-258.
  12. Mikkelsen, N.T., C. Schander, and E. Willassen, Local scale DNA barcoding of bivalves (Mollusca): A case study. Zoologica Scripta, 2007. 36(5): p. 455-463.
  13. Thomas-Chollier, M., L. Leyns, and V. Ledent, HoxPred: automated classification of Hox proteins using combinations of generalised profiles. Bmc Bioinformatics, 2007. 8.
  14. Fonseca, N.A., et al., Protein evolution of ANTP and PRD homeobox genes. Bmc Evolutionary Biology, 2008. 8.
  15. Frezal, L. and R. Leblois, Four years of DNA barcoding: Current advances and prospects. Infection Genetics and Evolution, 2008. 8(5): p. 727-736.
  16. Garcia-Espana, A., et al., Appearance of new tetraspanin genes during vertebrate evolution. Genomics, 2008. 91(4): p. 326-334.
  17. Olson, P.D., Hox genes and the parasitic flatworms: New opportunities, challenges and lessons from the free-living. Parasitology International, 2008. 57(1): p. 8-17.
  18. Rach, J., et al., Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proceedings of the Royal Society B-Biological Sciences, 2008. 275(1632): p. 237-247.
  19. Bergmann, T., et al., Character-based DNA barcoding: a superior tool for species classification. Berliner Und Munchener Tierarztliche Wochenschrift, 2009. 122(11-12): p. 446-450.
  20. Bertolazzi, P., G. Felici, and E. Weitschek, Learning to classify species with barcodes. Bmc Bioinformatics, 2009. 10.
  21. Camp, E., et al., Nanog Regulates Proliferation During Early Fish Development. Stem Cells, 2009. 27(9): p. 2081-2091.
  22. Jansen, G., R. Savolainen, and K. Vepsalainen, DNA barcoding as a heuristic tool for classifying undescribed Nearctic Myrmica ants (Hymenoptera: Formicidae). Zoologica Scripta, 2009. 38(5): p. 527-536.
  23. Kerr, K.C.R., et al., Filling the gap - COI barcode resolution in eastern Palearctic birds. Frontiers in Zoology, 2009. 6.
  24. Lemke, M.J., et al., Description of Freshwater Bacterial Assemblages from the Upper Parana River Floodpulse System, Brazil. Microbial Ecology, 2009. 57(1): p. 94-103.
  25. Lowenstein, J.H., G. Amato, and S.O. Kolokotronis, The Real maccoyii: Identifying Tuna Sushi with DNA Barcodes - Contrasting Characteristic Attributes and Genetic Distances. Plos One, 2009. 4(11).
  26. Shneyer, V.S., DNA barcoding of animal and plant species as an approach for their molecular identification and describing of diversity. Zhurnal Obshchei Biologii, 2009. 70(4): p. 296-315.
  27. Sirovich, L., M.Y. Stoeckle, and Y. Zhang, A Scalable Method for Analysis and Display of DNA Sequences. Plos One, 2009. 4(10).
  28. Wong, E.H.K., M.S. Shivji, and R.H. Hanner, Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach. Molecular Ecology Resources, 2009. 9: p. 243-256.
  29. Casiraghi, M., et al., DNA barcoding: a six-question tour to improve users' awareness about the method. Briefings in Bioinformatics, 2010. 11(4): p. 440-453.
  30. Karnkowska-Ishikawa, A., et al., TAXONOMY OF THE PHACUS OSCILLANS (EUGLENACEAE) AND ITS CLOSE RELATIVES-BALANCING MORPHOLOGICAL AND MOLECULAR FEATURES. Journal of Phycology, 2010. 46(1): p. 172-182.
  31. Machida, R.J. and A. Tsuda, Dissimilarity of Species and Forms of Planktonic Neocalanus Copepods Using Mitochondrial COI, 12S, Nuclear ITS, and 28S Gene Sequences. Plos One, 2010. 5(4).
  32. Naro-Maciel, E., et al., DNA barcodes for globally threatened marine turtles: a registry approach to documenting biodiversity. Molecular Ecology Resources, 2010. 10(2): p. 252-263.
  33. Pages, M., et al., Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries. Bmc Evolutionary Biology, 2010. 10.
  34. Pettengill, J.B. and M.C. Neel, AN EVALUATION OF CANDIDATE PLANT DNA BARCODES AND ASSIGNMENT METHODS IN DIAGNOSING 29 SPECIES IN THE GENUS AGALINIS (OROBANCHACEAE). American Journal of Botany, 2010. 97(8): p. 1391-1406.
  35. Undheim, E.A.B., et al., Genetic identification of Southern Ocean octopod samples using mtCOI. Comptes Rendus Biologies, 2010. 333(5): p. 395-404.