Comparative and Evolutionary Genomics

Motivation: An algorithm for comparative analysis of multiple trees reconstructed for representative protein families are discussed. This algorithm is based on the hypotheses of gene loss and horizontal gene transfers and uses stochastic methods and optimization. Some practical results are discussed. We describe a species tree comprising 40 prokaryotic organisms constructed by our algorithm on the basis of 132 individual groups of orthologous proteins (COGs) from GenBank of the National Center for Biotechnology Information (USA). We also describe a method for determination of horizontally transferred genes and its practical applications. Results: An algorithm for horizontal gene transfer determination is developed. Several horizontally transferred genes were detected using this algorithm. Availability: The software is available on request from the authors.