  In this article we are describing a new algorithm for detecting and
validating partial horizontal gene transfers (HGT). The presented algorithm is
based on a sliding window procedure which analyzes fragments of the given
multiple sequence alignment. A bootstrap procedure incorporated in our method
can be used to estimate the support of each inferred partial HGT. The new
algorithm can be also applied to confirm or discard complete (i.e.,
traditional) horizontal gene transfers detected by any HGT inferring algorithm.
While working on a full-genome scale, the introduced algorithm can be used to
assess the level of mosaicism of the whole species genomes as well as the rates
of complete and partial HGT underlying the evolution of the considered set of
species.
