Reconciliation with Non-binary Gene Trees Revisited

Abstract

By reconciling the phylogenetic tree of a gene family with the corresponding species tree, it is possible to infer lineage-specific duplications and losses with high confidence and hence annotate orthologs and paralogs. However, the currently available reconciliation methods for non-binary gene trees are computationally expensive for being applied on a genomic level. Here, an O|G|+|S| algorithm is presented to reconcile an arbitrary gene tree G with its corresponding species tree S, where |i¾ź| denotes the number of nodes in the corresponding tree. The improvement is achieved through two innovations: a fast computation of compressed child-image subtrees and efficient reconstruction of irreducible duplication histories.