About — PhyloCloud

What is PhyloCloud?

PhyloCloud is a web platform for storing, managing, annotating, and sharing annotated phylogenetic trees. It is designed for researchers who work with large collections of Newick-format trees and need a collaborative, reproducible way to organise and publish their data.

Trees are parsed and validated using ETE4, the fourth-generation Environment for Tree Exploration library. Annotations can be attached to any tree node and are stored in a structured, queryable format.

PhyloCloud is developed at the Comparative Genomics and Metagenomics Lab (CGM Lab) at the Centre for Plant Biotechnology and Genomics (CBGP) in Madrid, Spain.

Features

Upload & Store

Upload individual Newick files or bulk-import datasets. Trees are validated on upload.

Collections

Group related trees into named collections for projects or publications.

Annotations

Attach metadata to tree nodes via TSV files. Annotations are propagated automatically to internal nodes.

Full-Text Search

Filter and search across your trees and collections.

Public Sharing

Make trees publicly accessible so collaborators worldwide can discover and reuse your data.

Interactive Viewer

Visualise trees interactively in the browser using ETE4's SmartView renderer.

How to Cite

If you use PhyloCloud for research, please cite:

Tree annotation and visualization was performed using ETE Toolkit v4 [1] and TreeProfiler v2 [2] as implemented in PhyloCloud version 2 [3].

Huerta-Cepas J, Serra F, Bork P. ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol Biol Evol. 2016;33(6):1635–1638. doi:10.1093/molbev/msw046
Deng Z, Sanchis-López C, Hernández-Plaza A, Davín AA, Huerta-Cepas J. TreeProfiler: large-scale metadata profiling along gene and species trees. Mol Biol Evol. 2026;43(2):msag028. doi:10.1093/molbev/msag028
Deng Z, Botas J, Cantalapiedra CP, Hernández-Plaza A, Burguet-Castell J, Huerta-Cepas J. PhyloCloud: an online platform for making sense of phylogenomic data. Nucleic Acids Res. 2022;50(W1):W577–W582. doi:10.1093/nar/gkac324