Welcome to the Synteny Analysis Server

A computational platform for genome synteny analysis and species comparison

What Is This

This web server implements a pipeline designed to align DNA sequences pairwisely as described in Käther, K. K., Remmel, A., Lemke, S., & Stadler, P. F. (2025). Unbiased anchors for reliable genome-wide synteny detection. Algorithms for Molecular Biology, 20(1), 5. These alignments are high-confidence in the sense that almost all represent reciprocal best hits. They can be used to calculate collinear stretches of pairwise and multi-genome alignments, most prominently with MCScanX. The results include the alignments and instructions for calculating global synteny with MCScanX (see the tutorial). The alignments can additionally be used, with or without first computing collinearity chains, for enhanced orthology inference where genomic position is considered in addition to sequence similarity. Consult the tutorial and READMEs in the output for instructions and examples.

This service is freely available for academic research and educational purposes.

No registration or login required. All computational resources are provided at no cost to researchers worldwide. Content is licensed under Creative Commons Attribution 4.0 International License (CC BY 4.0). The underlying software has a separate open-source license.

Browse Species

View species with computed synteny anchors.

Browse Species

Download Sets

Download completed analysis sets containing synteny data for multiple species.

View Sets

Submit Analysis

Analyze your own genomes by uploading FASTA files or providing NCBI accessions.

Create New Job

Getting Started

Tutorial

Check out our Tutorial to see a Jupyter notebook displaying main downstream applications of AncST anchor alignments, including examples with MCScanX for synteny analysis and orthology inference workflows.

Usual Workflow

  1. Browse existing species and analysis sets
  2. To submit your own analysis, go to Create New Job
  3. Upload genome files (FASTA format) or provide NCBI accession numbers
  4. Configure analysis parameters or use automatic settings
  5. Receive email notifications when analysis is complete (optional)
  6. Access results via the provided bookmark link