A reliable ohnolog database yields insights into vertebrate evolution.

Notable changes: New feature: added the mem subcommand to mimic the bwa-mem command-line interface (CLI). Most input/output options and commonly used options are retained; unsupported or incompat...

Conservation success depends on translating theory into practical guidance and tools that are relevant and useful for non-scientists. While the complexity of population genetics has challenged the us...

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Abstract. The evolution of sexual dimorphism (the difference in average trait values between females and males, SD), is often thought to be constrained by

Communications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We prev...

The annotation of genomes lags behind their sequencing and assembly. For example, of 5,092 insect species in GenBank, as one of the most widely used databases, only 375 currently have annotated genome...

Abstract. Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously m

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

The fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organi...

This is a reference manual for the elegant, yet hideously complex concept of effective population size (Ne), inspired by a classic, self-published manual of automotive repair ‘for the compleat idiot’...

Traits that affect organismal fitness are often very genetically variable. This genetic variation is vital for populations to adapt to their environments, but it is also surprising given that nature (...

Standard methods for estimating the population recombination parameter, rho, are dependent on sampling individual genotypes and calculating various types of disequilibria. However, recent machine lear...

The concept of 'Differentially Expressed Genes' (DEGs) is central to RNA-Seq studies, yet their identification suffers from reproducibility issues. This is largely a consequence of the inherent…

VCFs are the most widely used data format for encoding genetic variation. By design, standard VCFs do not include data from sites where all individuals are homozygous for the reference allele ("invari...

Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, the...

Abstract. Selection often favors different trait values in males and females, leading to genetic conflicts between the sexes when traits have a shared gene

Seminar 9 John Werren (University of Rochester): Cooperating on Conflict: Selfish Genetic Elements, Heritable Microbes, and Genetic Conflicts. Bengt O. Bengtsson (Lund University): Decade…