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Large-scale multigene datasets used in phylogenomics and comparative genomics often contain sequence errors inherited from source genomes and transcriptomes. These errors typically manifest as stretches of non-homologous characters and derive from sequencing, assembly, and/or annotation errors. The lack of automatic tools to detect and remove sequence errors leads to the propagation of these errors in large-scale datasets. PREQUAL is a command line tool that identifies and masks regions with non-homologous adjacent characters in sets of
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