Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples
Determining the evolutionary history of a sampled sequence can become quite complex when multiple recombination events are part of its past. With at least five new recombination detection methods published in the last year, the growing list of over 40 methods suggests that this field is generating a lot of interest. In previous studies comparing recombination detection methods, the evaluation procedures did not measure how many recombinant sequences, breakpoints and donors were correctly identified. In this paper we will present the algorithm RecIdentify that scans a phylogenetic network and uses its edge lengths and topology to identify the parental/donor sequences and breakpoint positions for each query sequence. RecIdentify findings can be used to evaluate the output of recombination detection programs. RecIdentify may also assist in understanding how network size and complexity may shape recombination signals in a set of DNA sequences. The results may prove useful in the phylogenetic study of serially-sampled viral data with recombination events.
KeywordsQuery Sequence Phylogenetic Network Query Node Recombination Detection Dominance Rule
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- 1.Fan, J., Robertson, D.: Links to recombinant sequence analysis/detection programs (2006), http://bioinf.man.ac.uk/recombination/programs.shtml
- 2.Posada, D., Crandall, K.: The effect of recombination on the accuracy of phylogeny reconstruction. Journal of Molecular Evolution 54, 396–402 (2002)Google Scholar
- 3.Schierup, M., Hein, J.: Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879–891 (2000)Google Scholar
- 4.Worobey, M.: A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. Molecular Biology and Evolution 18, 1425–1434 (2001)Google Scholar
- 6.Wiuf, C., Christensen, T., Hein, J.: A simulation study of the reliability of recombination detection methods. Molecular Biology and Evolution 18, 1929–1939 (2001)Google Scholar
- 8.Lole, K.S., et al.: Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. Journal of Virology 73(1), 152–160 (1999)Google Scholar
- 9.Strimmer, K., et al.: A novel exploratory method for visual recombination detection. Genome Biology 4(5) (2003)Google Scholar
- 14.Siepel, A., Korber, B.: Scanning the Database for Recombinant HIV-1 Genomes. In: Human Retroviruses and AIDS Compendium Part III, pp. 35–60 (1995)Google Scholar