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, (iii) self-synteny, or (iv) FPC physical maps. It is designed for medium-to-high divergent eukaryotic genomes (not bacteria).

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

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

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

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

References:
C. Soderlund, M. Bomhoff, and W. Nelson (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Research 39(10):e68C. Link.

C. Soderlund, W. Nelson, A. Shoemaker and A. Paterson (2006) SyMAP: A system for discovering and viewing syntenic regions of FPC maps. Genome Research 16:1159-1168. Link.