… the distribution of paralogs in large gene families contains in itself sufficient phylogenetic
signal to infer fully resolved species phylogenies. This source of phylogenetic information is …

… used in phylogenomic inference: one that still includes only orthologs and one that includes
both orthologs and paralogs. We also describe the newly developed phylogenetic methods …

… in such analyses, but it is rarely assessed whether paralogous sequences have … the
phylogenetic reconstruction using a super-matrix approach. Herein, I tested the impact of paralogous …

… in the presence of NST signal arising from subsets of unrecognized paralogs genes within
… First, I consider phylogenetic analysis of concatenated alignments across putative orthologs. …

… As such, we recommend that phylogenomic analyses account for paralogs, such as through
our PPD tool, particularly when the study group of interest belongs to lineages where gene …

… Taking a phylogenomic approach and focusing on the Lissamphibia group, we test the
hypothesis that inadvertent paralog inclusion is driving the observed highly supported yet …

… phylogenomic complexity in Freziera, including the presence … that artifactual orthologs (ie,
the presence of only one copy of a … a negative impact on phylogenetic inference and support. …

… Unfortunately, rigorous phylogenetic analysis does not scale well computationally, making
it difficult to apply the most accurate tree reconstruction algorithms to large data sets [71,101]. …

… : from explicitly denoting them as paralogs, to randomly … analyses using single-copy orthologs.
Our results have significant implications for the use of ILS-aware phylogenomic analyses, …

… Here, we propose that the presence or absence of the C4 site functions as a binary switch
to modulate ar-C enhancer activity specific to one of two midline tissues after gene duplication. …