How to Use Foldtree
Commercially Available Online Web Server
Use Foldtree online for structure-based phylogenetic analysis of divergent protein families.
Foldtree builds phylogenetic trees from protein structure rather than sequence alone. That makes it valuable for protein families in which tertiary structure remains conserved deeper into evolutionary time than amino-acid identity, so a structure-based tree can recover relationships that sequence-only inference may blur or miss.
On Neurosnap, researchers can start from Input Uniprot IDs or upload their own Input Structures, which makes the service useful for both public-protein families and custom sets of predicted or engineered models. The workflow is especially relevant for remote homolog analysis, family diversification studies, and domains whose sequences are too diverged for a stable alignment-driven tree.
The output couples an interactive phylogeny with protein-level annotation summaries so structural relationships can be interpreted alongside the identities of the proteins being compared.
How Foldtree Works
Foldtree uses Foldseek-derived structure comparisons to build a pairwise similarity or distance matrix and then infers a phylogeny from that structural signal. This changes the question from 'which sequences align best?' to 'which folds and tertiary interaction patterns remain most similar?', which is often the more informative view in deep evolutionary problems.
On Neurosnap, UniProt input is convenient when public structures or predicted models can stand in for the family, while direct PDB input is better for custom ensembles, unpublished structures, or engineered variants. In either case, the resulting tree is best interpreted as a structure-informed evolutionary hypothesis rather than a replacement for every sequence-based analysis.
Researchers typically use Foldtree to identify broad clades, inspect structural outliers, and generate hypotheses that can later be checked against domain composition, function, or classical sequence phylogenies.
What is Neurosnap?
Neurosnap is the leading platform for bioinformatics and computational science focused on expanding access to powerful modeling and simulation tools. Because many state-of-the-art machine learning systems remain complex to install, configure, and scale, Neurosnap offers a clean, browser-based workspace that removes the burden of infrastructure management, dependency conflicts, and command-line tooling.
Built for biologists, chemists, and cross-disciplinary scientists, the platform enables advanced computational workflows without requiring expertise in software engineering or cloud architecture. Researchers can launch analyses through an intuitive interface, connect programmatically through a comprehensive API, and rely on automated resource management to scale workloads efficiently. By taking care of the underlying compute and operational complexity, Neurosnap allows teams to devote their energy to scientific progress and faster iteration. Security and data protection remain foundational principles, with clear safeguards outlined in our Terms of Use and Privacy Policy to ensure your work stays protected.
Advancing Discovery with Foldtree on Neurosnap
Using Foldtree on Neurosnap could drastically accelerate structure-based phylogenetic inference for remote homologs and divergent protein families.
- Flexible structural input: Foldtree supports both UniProt-based and direct structure-based entry points for evolutionary analysis.
- Deep-time signal: Structure can remain informative where sequence identity has eroded too far for comfortable alignment-based inference.
- Remote-homology utility: The method is well suited to families with conserved folds but weak primary-sequence similarity.
- Interactive interpretation: The tree and annotation summary make it easier to connect structural clades to biological hypotheses.
How to Use Foldtree on Neurosnap
To harness the capabilities of Foldtree, researchers can follow this streamlined workflow within Neurosnap:
- Access Neurosnap: Start by logging in to the Neurosnap website.
- Select Tool: From the list of available tools, choose Foldtree.
- Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
- Run Tool: Submit the Foldtree job and Neurosnap will execute it in the cloud, automatically notifying you as soon as your results are ready.
- Review Output: Explore your results through rich visualizations, including figures, plots, and interactive views designed to help you analyze findings with clarity and confidence.
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