The computation of phylogeny used to rely on sequence comparison (i.e. alignment). For genetically similar strains or species, there is typically only a few variations detectable in the aa/nt sequences of single-copy or selected gene list. On the other hand, the selection of gene list is also difficult. A prepared set of conserved genes can be efficient but may lead to bias. As an alternative, single-copy method can include more information, but a gene cannot be selected if it has no orthologs identified in the other strains/species. In case that recombination or horizontal transfer happened and even was involved in phenotype or adaptability of a pathogen, the transferred element would therefore not be included in the reconstruction of phylogeny. A problem in tracking the spread route can thus happen.

My question is: can it be possible to include genome recombination information into the reconstruction of phylogeny, or is there available method to select a suitable gene set for sequence alignment and phylogeny computation?

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