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csoderlund edited this page Oct 7, 2025 · 2 revisions

SyMAP - synteny computation with graphical query and display

Description: SyMAP (Synteny Mapping and Analysis Program) is a software package for detecting, displaying, and querying syntenic relationships between a fully sequenced genome and (i) another sequenced genome, (ii) draft sequence, and (iii) self-synteny. It is designed for divergent eukaryotic genomes (not bacteria).

Download SyMAP tarball: https://github.com/csoderlund/SyMAP/releases. The SyMAP tarball contains the executable jar file, all necessary external software, and demo files.

Requirements: Java v17 or later and MySQL (or MariaDB). SyMAP uses MUMmer for the sequence to sequence alignment, which requires Perl.
SyMAP has been tested on Linux and MacOS.

To use:

  1. Download the latest SyMAP tarball.
  2. Put the tarball in the location you want the symap_5 directory and untar it (tar xf symap_5.tar.gz).
  3. Follow the instructions in https://csoderlund.github.io/SyMAP/SystemGuide.html#demo to try the demo.

Full Documentation: https://csoderlund.github.io/SyMAP

SyMAP github code: To build, see SyMAP/java/README.

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