Gene families evolve by the processes of speciation (creating orthologs), gene duplication
(paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and …

Plant genome sequencing has dramatically increased, and some species even have
multiple high-quality reference versions. Demands for clade-specific homology inference …

Accurate determination of the evolutionary relationships between genes is a foundational
challenge in biology. Homology—evolutionary relatedness—is in many cases readily …

Abstract The Alliance of Genome Resources (Alliance) is an extensible coalition of
knowledgebases focused on the genetics and genomics of intensively studied model …

Background Ab initio prediction of splice sites is an essential step in eukaryotic genome
annotation. Recent predictors have exploited Deep Learning algorithms and reliable gene …

Background The draft genome assemblies produced by new sequencing technologies
present important challenges for automatic gene prediction pipelines, leading to less …

Prediction of orthologs is an important bioinformatics pursuit that is frequently used for
inferring protein function and evolutionary analyses. The InParanoid database is a well …

What makes a mouse a mouse, and not a hamster? Differences in gene regulation between
the two organisms play a critical role. Comparative analysis of gene coexpression networks …

Orthology assignment is a key step of comparative genomic studies, for which many
bioinformatic tools have been developed. However, all gene clustering pipelines are based …

Accurate inference of orthologous genes constitutes a prerequisite for comparative and
evolutionary genomics. SonicParanoid is one of the fastest tools for orthology inference; …