Documentation: www.agcol.arizona.edu/software/symap. It is also available in the /doc directory for local viewing.
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.
Description: SyMAP (Synteny Mapping and Analysis Program) is a software package for detecting, displaying, and querying syntenic relationships between sequenced chromosomes and/or FPC physical maps. It is designed for medium-to-high divergent eukaryotic genomes (not bacteria). It can align a draft genome to a fully sequenced genome, but not draft-to-draft.
Requirements: Java v1.7 or later and MySQL. SyMAP uses MUMmer for the sequence to sequence alignment, which requires Perl. SyMAP has been tested on Linux and MacOSX.
SyMAP package: The SyMAP package contains the jar files, external packages and demo files.
SyMAP github code: This site contains all necessary external classes and packages. To install, see SyMAP/java/README.