SyMAP (Synteny Mapping and Analysis Program) is a software package for detecting, displaying, and querying syntenic relationships between sequenced genomes.
It is designed for medium-to-high divergent eukaryotic genomes (not bacteria).
It can align a draft genome to a fully sequenced genome (see peach), but not draft-to-draft.
It can perform self-synteny. It can align to FPC physical maps.
Releases v5.1.0 and later are available from the Github links below.
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):e68 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
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