Phylogenetic tree reconciliation is the method of choice in analysing host-symbiont systems. Despite the many reconciliation tools that have been proposed in the literature, two main issues remain unresolved: listing suboptimal solutions (i.e., whose score is “close” to the optimal ones), and listing only solutions that are biologically different “enough”. The first issue arises because the optimal solutions are not always the ones biologically most significant; providing many suboptimal solutions as alternatives for the optimal ones is thus very useful. The second one is related to the difficulty to analyse an often huge number of optimal solutions. Capybara addresses both of these problems in an efficient way. Furthermore, it includes a tool for visualising the solutions that significantly helps the user in the process of analysing the results.
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