StepBrothers: inferring partially shared ancestries among recombinant viral sequences.

ABSTRACT: Phylogeneticists have developed several statistical methods to infer recombination among molecular sequences that are evolutionarily related. Of these methods, Markov change-point models currently provide the most coherent framework. Yet, the Markov assumption is faulty in that the inferred relatedness of homologous sequences across regions divided by recombinant events is not independent, particularly for nonrecombinant sequences as they share the same history. To correct this limitation, we introduce a novel random tips (RT) model. The model springs from the idea that a recombinant sequence inherits its characters from an unknown number of ancestral full-length sequences, of which one only observes the incomplete portions. The RT model decomposes recombinant sequences into their ancestra

SUBMITTER: Bloomquist EW 

PROVIDER: S-EPMC2639346 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature