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- person_outline Brigitte Boeckmann
Publication for SwissTree
GATC: a genetic algorithm for gene tree construction under the Duplication Transfer Loss model of evolution
[…] ) and the V-type ATPase beta subunit (VATP).These gene families have been re-analyzed here to assess the performance of GATC on an empirical dataset. The reference species tree used was obtained from SwissTree . Protein sequences from genomes not found in the species tree were removed and the remaining sequences aligned with Muscle . GATC was used to reconstruct the corresponding trees for eac […]
Towards Consensus Gene Ages
[…] We inferred the ages for each gene by mapping the species in that gene’s ortholog group onto a reference species tree from SwissTree, which was derived from a consensus of trees found in the literature (). The age of a protein is calculated on the species tree by finding the MRCA node of the taxa that have orthologs of th […]
Standardised Benchmarking in the Quest for Orthologs
[…] anual oversight is expected to yield gene phylogenies with high statistical support and topological consistency.Concordance of orthology predictions was assessed with two sets of trees. The first was SwissTree,, a small collection of large and high-confidence gene family phylogenies with different types of challenges for orthology prediction and species from all domains. The second, TreeFam-A, con […]
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