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MOTIVATION Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome(More)
—Phylogenetic inference is the process of reconstructing the evolutionary history of species based on their traits, nowadays mostly using molecular sequence data. Current state-of-the-art inference methods, like Bayesian and Maximum Likelihood (ML) inference, rely on the Phylogenetic Likelihood Function (PLF) as their computational core. Due to the large(More)
Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic(More)
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