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Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distancedoi:10.1007/978-1-61779-585-5_3 pmid:22399455 pmcid:PMC3842619 fatcat:xx55mye7nraxrfwgg3pgtzh7em