Summary
Sequences subject to recombination and gene conversion defy phylogenetic analysis by traditional methods since their evolutionary history cannot be adequately summarized by a tree. This study investigates ways to describe their evolutionary history and proposes a method giving a partial reconstruction of this history. Multigene families, viruses, and alleles from within populations experience recombinations/gene conversions, so the questions studied here are relevant for a large body of data and the suggested solutions should be very practical. The method employed was implemented in a program, RecPars, written in C and was used to analyze nine retroviruses.
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Hein, J. A heuristic method to reconstruct the history of sequences subject to recombination. J Mol Evol 36, 396–405 (1993). https://doi.org/10.1007/BF00182187
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DOI: https://doi.org/10.1007/BF00182187