PhylomeDB

PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed, genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interests. The v5 release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogeniesPhylomeDB是一款独特的公共知识库，面向公众开放可挖掘、可浏览的预计算全基因组同源基因注释序列、序列比对及系统发育组（phylome）集合目录，同时配套提供基于系统发育的直系同源与旁系同源关系数据。此外，用户可下载PhylomeDB的系统发育树与序列比对结果，用于进一步分析：包括检测基因复制事件并确定其发生时间、推断物种间杂交与水平基因转移的历史事件，以及挖掘目标基因与生物体所经历的选择作用、基因渐渗、基因转换及其他相关进化过程的痕迹。其v5版本实现了核心数据规模的大幅扩容，目前该库可访问534个系统发育组，涵盖超过800万棵系统发育树，并为超过6000个物种的基因提供同源关系数据。这使得PhylomeDB成为目前规模最大、内容最全面的公共基因系统发育数据库。

搜集汇总

背景与挑战

背景概述

PhylomeDB是一个公共数据库，专门提供基因系统发育（phylomes）的完整目录，包括系统发育树、多序列比对以及基于系统发育的直系同源和旁系同源关系预测。它支持数据下载和交互式可视化，并包含大量预计算数据，如534个phylomes、超过800万棵树和6000多个物种的基因同源关系，使其成为最大的公共基因系统发育存储库。