Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28223 Madrid, Spain.
Nucleic Acids Res. 2022 Jul 5;50(W1):W577-W582. doi: 10.1093/nar/gkac324.
Phylogenomics data have grown exponentially over the last decades. It is currently common for genome-wide projects to generate hundreds or even thousands of phylogenetic trees and multiple sequence alignments, which may also be very large in size. However, the analysis and interpretation of such data still depends on custom bioinformatic and visualisation workflows that are largely unattainable for non-expert users. Here, we present PhyloCloud, an online platform aimed at hosting, indexing and exploring large phylogenetic tree collections, providing also seamless access to common analyses and operations, such as node annotation, searching, topology editing, automatic tree rooting, orthology detection and more. In addition, PhyloCloud provides quick access to tools that allow users to build their own phylogenies using fast predefined workflows, graphically compare tree topologies, or query taxonomic databases such as NBCI or GTDB. Finally, PhyloCloud offers a novel tree visualisation system based on ETE Toolkit v4.0, which can be used to explore very large trees and enhance them with custom annotations and multiple sequence alignments. The platform allows for sharing tree collections and specific tree views via private links, or make them fully public, serving also as a repository of phylogenomic data. PhyloCloud is available at https://phylocloud.cgmlab.org.
过去几十年来，系统发育基因组学数据呈指数级增长。目前，全基因组项目生成数百甚至数千个系统发育树和多个序列比对是很常见的，这些树和比对可能也非常大。然而，此类数据的分析和解释仍然依赖于定制的生物信息学和可视化工作流程，非专业用户很难实现这些流程。在这里，我们介绍了 PhyloCloud，这是一个在线平台，旨在托管、索引和探索大型系统发育树集合，并提供对常见分析和操作（如节点注释、搜索、拓扑编辑、自动树系根、同源检测等）的无缝访问。此外，PhyloCloud 还提供了快速访问工具的途径，这些工具允许用户使用快速预定义的工作流程构建自己的系统发育树，图形化比较树拓扑，或查询 NBCI 或 GTDB 等分类数据库。最后，PhyloCloud 提供了一个基于 ETE Toolkit v4.0 的新型树可视化系统，可用于探索非常大的树，并使用自定义注释和多个序列比对来增强它们。该平台允许通过私有链接共享树集合和特定的树视图，或使其完全公开，同时也作为系统发育基因组学数据的存储库。PhyloCloud 可在 https://phylocloud.cgmlab.org 上访问。
