Orthoweb: a software package for evolutionary analysis of gene networks.

Abstract

This article introduces Orthoweb (https://orthoweb.sysbio.cytogen.ru/), a software package developed for the calculation of evolutionary indices, including phylostratigraphic indices and divergence indices (Ka/Ks) for individual genes as well as for gene networks. The phylostratigraphic age index (PAI) allows the evolutionary stage of a gene's emergence (and thus indirectly the approximate time of its origin, known as "evolutionary age") to be assessed based on the analysis of orthologous genes across closely and distantly related taxa. Additionally, Orthoweb supports the calculation of the transcriptome age index (TAI) and the transcriptome divergence index (TDI). These indices are important for understanding the dynamics of gene expression and its impact on the development and adaptation of organisms. Orthoweb also includes optional analytical features, such as the ability to explore Gene Ontology (GO) terms associated with genes, facilitating functional enrichment analyses that link evolutionary origins of genes to biological processes. Furthermore, it offers tools for SNP enrichment analysis, enabling the users to assess the evolutionary significance of genetic variants within specific genomic regions. A key feature of Orthoweb is its ability to integrate these indices with gene network analysis. The software offers advanced visualization tools, such as gene network mapping and graphical representations of phylostratigraphic index distributions of network elements, ensuring intuitive interpretation of complex evolutionary relationships. To further streamline research workflows, Orthoweb includes a database of pre-calculated indices for numerous taxa, accessible via an application programming interface (API). This feature allows the users to retrieve pre-computed phylostratigraphic and divergence data efficiently, significantly reducing computational time and effort.