PhyloCloud PhyloCloud v2.0

PhyloCloud

Upload, annotate, visualise, and share phylogenetic trees — from a single Newick file to genome-scale datasets with hundreds of thousands of leaves. Powered by ETE4 SmartView.

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Collection A Collection B

Manage Trees and Collections

Upload Newick, NHX, or annotated .ete files. Organise trees into named collections for publications or projects. Set public, unlisted, or private access per tree.

Bacteria Archaea Eukaryota Viruses

Visualize

Newick tree visualisation powered by ETE4 SmartView. Build annotation panels with heatmaps, bar plots, PA matrices, domain tracks, taxonomy colouring, and more — all configurable from a live layout editor.

OG OG

Analyze Coming soon

Phylogenetic analysis workflows: annotate clades with Pfam domains, multiple-sequence alignments, taxonomic lineages, and orthology groups. Propagate summaries from leaves to internal nodes automatically.

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].

  1. 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
  2. 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
  3. 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

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