Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Preprocessing and feature extraction

G-Aligner

An open-source graph-based method for aligning untargeted LC-MS features across runs by solving the correspondence problem as a multidimensional assignment task.

LC-MSUntargeted metabolomicsPython packageCommand lineOpen source
Access toolSuggest an update

Overview

G-Aligner aligns previously detected LC-MS features across runs using a multipartite-graph formulation of feature correspondence. It optimizes competing matches using m/z, retention time and abundance information rather than extracting peaks from raw files.

What can this tool do?

Retention-time alignment

Common uses

  • Align extracted LC-MS features across multiple samples or runs.
  • Replace or compare alignment stages from preprocessing workflows such as XCMS, OpenMS, or MZmine.

Scientific fit

Primary function

Preprocessing and feature extraction

Analysis types

Untargeted metabolomics

Data compatibility

Inputs

Feature or peak table

Outputs

Feature or peak table

Input formats

CSV or TSV

Output formats

CSV or TSV

Scope and considerations

Designed for

  • Cross-run feature alignment after feature extraction in untargeted LC-MS.

Not designed for

  • Raw-data peak detection or identification of the molecules represented by aligned features.

Important requirements

  • Python environment, the supplied third-party solver components and per-run CSV feature lists with m/z, retention time and area columns; adjust the example configuration for the study.

Considerations

  • Poor upstream detection or inappropriate alignment tolerances can propagate into correspondence results; inspect missingness and ambiguous matches after alignment.

Access and documentation

Primary accessDocumentation

The official README states MulanPSL-2.0. Installation includes separately installed solver components whose requirements should also be checked.

License: MulanPSL-2.0

Evidence and review

Enveda intake rechecked against official README/documentation, repository access terms and primary publication metadata on 2026-10-27. Editorial source review only; no software execution or independent benchmarking. See docs/enveda-expansion-review-2026-10-27.md.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. G-Aligner: a graph-based feature alignment method for untargeted LC–MS-based metabolomics. BMC Bioinformatics (2023). doi:10.1186/s12859-023-05525-4

Related tools

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Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-27 · First committed entry

    Add 27 source-reviewed tools from Enveda intake

    View change · Entry at this revision

Full GitHub history