Reproducibility Data for Evolutionary Expansion and Functional Retention of Immune-Related Duplicate Gene Families in Cyprinid Fishes

<p dir="ltr">This repository contains the processed datasets, intermediate analysis files, and computational scripts supporting the study <b>"Evolutionary Expansion and Functional Retention of Immune-Related Duplicate Gene Families Following Whole-Genome Duplication in Cyprinid Fishes."</b></p><p dir="ltr">The dataset provides the resources required to reproduce the comparative genomic, evolutionary, and functional analyses performed in this study.

The repository includes OrthoFinder-based orthogroup assignments and gene count matrices, immune-related functional annotation results generated using eggNOG-mapper, processed duplication and synteny analysis outputs, Ka/Ks-based molecular evolution analyses, phylogenetic reconstruction files generated using IQ-TREE, functional enrichment results, CAFE5-related gene family evolution outputs, and custom Python scripts used for data processing and visualization.</p><p dir="ltr">Genome assemblies and protein sequence resources analyzed in this study were obtained from publicly available databases and were not redistributed in this repository.