How orthologs are inferred in TreeFam?

In TreeFam, orthologs and within-species paralogs are inferred from phylogenetic trees. Two genes are said to be orthlogs if they are both present in a gene tree and their last common ancestor (LCA) in the gene tree is a speciation node. Within-species paralogs are more obvious from trees, and we further provide the ancestral species from which the paralogs were originated.

For a TreeFam-A family, we merge the constrained full tree and the clean tree to utilize curation information, and for a TreeFam-B family, we use the clean tree directly. We then use a multifurcated species tree to infer duplication events and orthologs. The species tree used here (below) contains more polytomies (multifurcated nodes) than the tree used to infer duplications displayed in TreeFam web site.

Polytomies lead to the loss of some information, but they help to infer correct orthologs even if the gene tree contains wrong branches. The `score' in the TreeFam gene page is bootstrapping supports rescaled ... more.

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